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add protein and ligand

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lingyuzeng
2024-09-19 21:12:59 +08:00
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script/S112D/Conformer3D_COMPOUND_CID_2733285.gro Normal file
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Conformer3D_COMPOUND_CID_2733285
35
1MOL N 1 -0.539 0.212 -0.953
1MOL N 2 -1.066 0.319 -0.942
1MOL N 3 -1.349 0.194 -1.089
1MOL C 4 -0.707 0.366 -0.976
1MOL C 5 -0.661 0.237 -0.951
1MOL C 6 -0.753 0.135 -0.922
1MOL C 7 -0.889 0.163 -0.919
1MOL C 8 -0.935 0.292 -0.945
1MOL C 9 -0.844 0.394 -0.973
1MOL C 10 -1.141 0.309 -1.056
1MOL C 11 -1.207 0.178 -1.092
1MOL C 12 -1.163 0.136 -1.232
1MOL C 13 -1.044 0.042 -1.222
1MOL C 14 -0.921 0.109 -1.282
1MOL C 15 -1.074 -0.087 -1.298
1MOL O 16 -0.454 0.307 -0.982
1MOL O 17 -0.496 0.091 -0.927
1MOL O 18 -1.154 0.405 -1.129
1MOL H01 19 -0.636 0.446 -0.999
1MOL H02 20 -0.717 0.034 -0.902
1MOL H03 21 -0.960 0.084 -0.897
1MOL H04 22 -0.879 0.495 -0.994
1MOL H05 23 -1.177 0.101 -1.020
1MOL H06 24 -1.135 0.224 -1.290
1MOL H07 25 -1.246 0.085 -1.282
1MOL H08 26 -1.025 0.018 -1.118
1MOL H09 27 -0.837 0.039 -1.280
1MOL H10 28 -0.942 0.137 -1.385
1MOL H11 29 -0.896 0.198 -1.224
1MOL H12 30 -1.162 -0.071 -1.362
1MOL H13 31 -0.989 -0.113 -1.361
1MOL H14 32 -1.094 -0.167 -1.228
1MOL H 33 -1.111 0.347 -0.855
1MOL H 34 -1.377 0.233 -0.999
1MOL H 35 -1.377 0.264 -1.158
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

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http://bbs.keinsci.com/thread-45791-1-1.html
https://www.jianshu.com/p/d1ae60c96b33
Sobtop（http://sobereva.com/soft/Sobtop）
这是我开发的GROMACS拓扑文件产生工具，主要产生GAFF、AMBER力场的拓扑文件，但由于其力场库可以自行非常方便地修改和扩充，因此Sobtop本质上是完全普适、通用的。Sobtop可谓是最理想、最灵活、最易用的产生GROMACS拓扑文件的工具。此程序用起来超级简单，什么额外的程序以及特殊的运行环境都不需要装，解压即用。Sobtop使用极其方便，照着屏幕上的提示敲几下键盘，itp、top和gro文件就产生了，另外也可以要求产生rtp文件。Sobtop的主页有非常详细的产生各类体系拓扑文件的例子，并给出了详细的相关要点的说明。从例子中你会体会到Sobtop的设计特别注重兼顾便利和灵活，初级用户会体会到它极其便利，而高级用户则会体会到通过Sobtop构建复杂体系拓扑文件特别灵活好用。
[下载](https://cloud.189.cn/t/MbiQ3yjMjmMr)（访问码：npg8）

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script/S112D/S112D.sh Executable file
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#!/bin/bash
#This script needs to be edited for each run.
#Define PDB Filename & GROMACS Pameters
# reference: http://www.mdtutorials.com/gmx/lysozyme/
# NAME=1ao7 NSTEPS=50000000 ./md_gromacs.sh
# 命令会临时设置 NAME 为 1ao7 和 NSTEPS 为 50000000（对应 100ns），然后运行 md_gromacs.sh 脚本
# Check if GMXRC_PATH is provided and source it
if [ -n "$GMXRC_PATH" ]; then
source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
fi
GPU_ID=${GPU_ID:-"0"}
NAME=${NAME:-"S112D-Alphafold2"}
LIGAND_GRO="ligand.gro" # 配体的 .gro 文件
LIGAND_ITP="ligand.itp" # 配体的 .itp 文件
# FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
FORCEFIELD=${FORCEFIELD:-"amber99sb"}
WATERMODEL=${WATERMODEL:-"tip3p"}
WATERTOPFILE=${WATERTOPFILE:-"spc216.gro"}
BOXTYPE=${BOXTYPE:-"tric"}
BOXORIENTATION=${BOXORIENTATION:-"1.0"}
# NSTEPS=${NSTEPS:-500000} # 50,000 steps for 1 ns
NSTEPS=${NSTEPS:-50000000} # 100 ns 模拟
DT=${DT:-0.002} # 2 fs
#BOXSIZE="5.0"
#BOXCENTER="2.5"
# Define simulation name variable
MDRUN_NAME=${MDRUN_NAME:-"md"}
NDX_NAME=${NDX_NAME:-"index"}
# Define analysis parameters
# Define other filenames based on MDRUN_NAME
TPR_FILE="${MDRUN_NAME}.tpr"
XTC_FILE="${MDRUN_NAME}.xtc"
NDX_FILE="${NDX_NAME}.ndx"
NO_PBC_XTC_FILE="${MDRUN_NAME}_noPBC.xtc"
OUTPUT_FOLDER=${OUTPUT_FOLDER:-"frame_extraction_output"}
TEMP_FOLDER=${TEMP_FOLDER:-"temp"}
# Define variables for frame extraction
EXTRACT_EVERY_PS=${EXTRACT_EVERY_PS:-100} # Default to 100 ps if not set
# Print the current settings
echo "Current settings:"
echo "NAME: $NAME"
echo "LIGAND_GRO: $LIGAND_GRO"
echo "FORCEFIELD: $FORCEFIELD"
echo "WATERMODEL: $WATERMODEL"
echo "WATERTOPFILE: $WATERTOPFILE"
echo "BOXTYPE: $BOXTYPE"
echo "BOXORIENTATION: $BOXORIENTATION"
echo "NSTEPS: $NSTEPS"
echo "DT: $DT"
echo "MDRUN_NAME: $MDRUN_NAME"
echo "TPR_FILE: $TPR_FILE"
echo "XTC_FILE: $XTC_FILE"
echo "NO_PBC_XTC_FILE: $NO_PBC_XTC_FILE"
echo "OUTPUT_FOLDER: $OUTPUT_FOLDER"
echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS"
# Step 1: Generate GROMACS .gro file for the protein
gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -p topol.top -ignh
# gmx_mpi pdb2gmx -f protein.pdb -o protein.gro -ff $FORCEFIELD -water $WATERMODEL -p topol.top -ignh
# Step 2: Merge protein and ligand .gro files into a complex
cat protein.gro mol.gro > complex.gro
# 获取蛋白质和小分子的原子数
PROTEIN_ATOMS=$(head -n 2 protein.gro | tail -n 1 | tr -d ' ')
LIGAND_ATOMS=$(head -n 2 mol.gro | tail -n 1 | tr -d ' ')
# 打印原子数，确保正确
echo "Protein atoms: $PROTEIN_ATOMS"
echo "Ligand atoms: $LIGAND_ATOMS"
# 计算总原子数
TOTAL_ATOMS=$(($PROTEIN_ATOMS + $LIGAND_ATOMS))
# 打印总原子数
echo "Total atoms: $TOTAL_ATOMS"
# Update the atom count in the complex.gro file
sed -i "2s/\(^[[:space:]]*\)[0-9]\+/\1$TOTAL_ATOMS/" complex.gro
echo -e "0\nq" | gmx_mpi genrestr -f mol.gro -o posre_mol.itp
cat << EOF >> mol.itp
#ifdef POSRES
#include "posre_mol.itp"
#endif
EOF
# Modify the topology file to include the ligand
# echo "#include \"$LIGAND_ITP\"" >> topol.top
# Step 6: Modify the topology file to include the ligand and its parameters
# 6.1 在topol.top顶部添加小分子的参数文件
sed -i '/^; Include forcefield parameters/a #include "jz4.prm"' topol.top
# 6.2 在position restraint后添加小分子的拓扑文件
sed -i '/^; Include Position restraint file/!b;n;/#endif/a ; Include ligand topology\n#include "jz4.itp"' topol.top
# 6.3 在[molecules]部分添加小分子
sed -i '/^Protein_chain_A/a JZ4 1' topol.top
# Step 3: Define the simulation box
gmx_mpi editconf -f complex.gro -o complex-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION
# Step 4: Add solvate
gmx_mpi solvate -cp complex-box.gro -cs $WATERTOPFILE -o complex-solv.gro -p topol.top
# add icons # ! ions.mdp add by manual
# --- ions.mdp file content --- #
cat << EOF > ions.mdp
; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm （steep = steepest descent minimization）
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of （minimization） steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list （simple, grid）
coulombtype = cutoff ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
EOF
gmx_mpi grompp -f ions.mdp -c complex-solv.gro -p topol.top -o ions.tpr -maxwarn 1
echo SOL | gmx_mpi genion -s ions.tpr -o complex-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral
# energy minimization of the structure in solvate # ! minim.mdp add by manual
# --- minim.mdp file content --- #
cat << EOF > minim.mdp
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm （steep = steepest descent minimization）
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of （minimization） steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list （simple, grid）
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
EOF
gmx_mpi grompp -f minim.mdp -c complex-solv-ions.gro -p topol.top -o em.tpr
gmx_mpi mdrun -v -deffnm em
# optional em, you will need the Xmgrace plotting too
#gmx_mpi energy -f em.edr -o potential.xvg
#position restrain
# gmx_mpi grompp -f posre.mdp -c em.gro -p topol.top -o posre.tpr -r em.gro
# gmx_mpi mdrun -v -deffnm posre
# nvt
# gmx_mpi grompp -f nvt.mdp -c posre.gro -p topol.top -o nvt.tpr
# --- nvt.mdp file content --- #
cat << EOF > nvt.mdp
title = OPLS Lysozyme NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff （in nm）
rvdw = 1.0 ; short-range van der Waals cutoff （in nm）
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
EOF
gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
gmx_mpi mdrun -v -deffnm nvt
# optional : Let's analyze the temperature progression, again using energy:
# gmx_mpi energy -f nvt.edr -o temperature.xvg
# npt
# gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
# --- npt.mdp file content --- #
cat << EOF > npt.mdp
title = OPLS Lysozyme NPT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; Velocity generation is off
EOF
gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx_mpi mdrun -v -deffnm npt
# Optional: Let's analyze the pressure progression, again using energy: type 18 0
# gmx energy -f npt.edr -o pressure.xvg
# Optional: Let's take a look at density as well, this time using energy and entering "24 0" at the prompt.
# gmx energy -f npt.edr -o density.xvg
# md
# --- md.mdp file content --- #
cat << EOF > ${MDRUN_NAME}.mdp
title = OPLS Lysozyme NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = ${NSTEPS} ; steps for simulation
dt = ${DT} ; time step in fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff （in nm）
rvdw = 1.0 ; short-range van der Waals cutoff （in nm）
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
EOF
# Generate GROMACS .tpr file for the simulation
gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}
# Run the simulation
gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1 -gpu_id ${GPU_ID}
# gmx_mpi rms -f md.xtc -s md.tpr -o rmsd_protein.xvg
# 两次都选骨架部分（protein）
# 注意观测在模拟过程中骨架的RMSD波动是否较大
# gmx_mpi rms -f md.xtc -s md.tpr -o rmsd_protein.xvg
# 第一次选择骨架部分（protein）第二次选择配体（MOL）
# 可以消除蛋白质整体的运动，观察小分子配体相对于蛋白质的运动
# extra ndx file , select protein
echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}
# echo -e "1\nq" | gmx_mpi make_ndx -f md.gro -o index.ndx
# Create extraction output directory
mkdir -p ${OUTPUT_FOLDER}
# Create temp output directory
mkdir -p ${TEMP_FOLDER}
echo -e "1\nq" | gmx_mpi trjconv -dt ${EXTRACT_EVERY_PS} -s ${TPR_FILE} -f ${XTC_FILE} -n ${NDX_FILE} -pbc mol -o ${TEMP_FOLDER}/temp.xtc
# echo -e "1\nq" | gmx_mpi trjconv -dt 100 -s md.tpr -f md.xtc -n index.ndx -pbc mol -o temp/temp.xtc
echo -e "1\n1\n1" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -o ${TEMP_FOLDER}/traj_show.xtc
# echo -e "1\n1\n1" | gmx_mpi trjconv -s md.tpr -f temp/temp.xtc -n index.ndx -center -fit rot+trans -o temp/traj_show.xtc
echo -e "1\n1\n1" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -b 0 -e 0 -o ${TEMP_FOLDER}/tarj_show.pdb
# echo -e "1\n1\n1" | gmx_mpi trjconv -s md.tpr -f temp/temp.xtc -n index.ndx -center -fit rot+trans -b 0 -e 0 -o temp/tarj_show.pdb
# Group 1 ( Protein)
# ---
# Step 1: Extract frames every 1000 ps
gmx_mpi trjconv -s ${TPR_FILE} -f ${XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -dt ${EXTRACT_EVERY_PS} -pbc mol <<EOF
0
EOF
# Step 2: Center and fit the trajectory
# Centering the protein and fitting to the initial frame
gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -pbc mol -center <<EOF
1
1
EOF
# Step 3: Output PDB format file
gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${MDRUN_NAME}.pdb -pbc mol -center <<EOF
1
0
EOF
# Continue with further analysis like RMSD calculation...
# ... [other analysis commands] ...
# End of script
# command reference
# Command 1: 提取蛋白质
command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
# echo "Protein": 选择蛋白质组，用于告诉 gmx trjconv 要处理哪个部分。
# -dt 1000: 指定时间间隔（这里是1000 picoseconds），用于从 .xtc 文件中抽取帧。
# -s {tpr_file}: 指定拓扑文件（.tpr），它包含了模拟系统的完整描述。
# -f {xtc_file}: 指定原始的 .xtc 轨迹文件。
# -n {temp_folder}/tarj_show.ndx: 指定索引文件，其中包含各种原子群的定义。
# -pbc mol: 处理周期性边界条件，确保分子不会被分割。
# -o {temp_folder}/temp.xtc: 指定输出文件名和位置。
# Command 2: 中心对齐蛋白质
command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
# echo "Protein\nProtein\nProtein": 三次选择蛋白质组，分别用于中心化、拟合和输出。
# -center: 将蛋白质移动到框架的中心。
# -fit rot+trans: 对齐蛋白质，通过旋转和平移来最佳拟合。
# -o {output_folder}/traj_show.xtc: 指定输出文件名和位置。
# Command 3: 抽取帧生成 .pdb 文件
command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb'
# -b 0 -e 0: 指定开始和结束时间，这里设置为0表示只取第一帧。
# -o {output_folder}/tarj_show.pdb: 输出为 .pdb 格式，存储在指定的位置。

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Conformer3D_COMPOUND_CID_2733285
35
1MOL N 1 -0.539 0.212 -0.953
1MOL N 2 -1.066 0.319 -0.942
1MOL N 3 -1.349 0.194 -1.089
1MOL C 4 -0.707 0.366 -0.976
1MOL C 5 -0.661 0.237 -0.951
1MOL C 6 -0.753 0.135 -0.922
1MOL C 7 -0.889 0.163 -0.919
1MOL C 8 -0.935 0.292 -0.945
1MOL C 9 -0.844 0.394 -0.973
1MOL C 10 -1.141 0.309 -1.056
1MOL C 11 -1.207 0.178 -1.092
1MOL C 12 -1.163 0.136 -1.232
1MOL C 13 -1.044 0.042 -1.222
1MOL C 14 -0.921 0.109 -1.282
1MOL C 15 -1.074 -0.087 -1.298
1MOL O 16 -0.454 0.307 -0.982
1MOL O 17 -0.496 0.091 -0.927
1MOL O 18 -1.154 0.405 -1.129
1MOL H01 19 -0.636 0.446 -0.999
1MOL H02 20 -0.717 0.034 -0.902
1MOL H03 21 -0.960 0.084 -0.897
1MOL H04 22 -0.879 0.495 -0.994
1MOL H05 23 -1.177 0.101 -1.020
1MOL H06 24 -1.135 0.224 -1.290
1MOL H07 25 -1.246 0.085 -1.282
1MOL H08 26 -1.025 0.018 -1.118
1MOL H09 27 -0.837 0.039 -1.280
1MOL H10 28 -0.942 0.137 -1.385
1MOL H11 29 -0.896 0.198 -1.224
1MOL H12 30 -1.162 -0.071 -1.362
1MOL H13 31 -0.989 -0.113 -1.361
1MOL H14 32 -1.094 -0.167 -1.228
1MOL H 33 -1.111 0.347 -0.855
1MOL H 34 -1.377 0.233 -0.999
1MOL H 35 -1.377 0.264 -1.158
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

350
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; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev5) on 2024-09-19
[ atomtypes ]
; name at.num mass charge ptype sigma (nm) epsilon (kJ/mol)
no 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01
n 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01
n3 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01
ca 6 12.010736 0.000000 A 3.399670E-01 3.598240E-01
c 6 12.010736 0.000000 A 3.399670E-01 3.598240E-01
c3 6 12.010736 0.000000 A 3.399670E-01 4.577296E-01
o 8 15.999405 0.000000 A 2.959922E-01 8.786400E-01
ha 1 1.007941 0.000000 A 2.599642E-01 6.276000E-02
h1 1 1.007941 0.000000 A 2.471353E-01 6.568880E-02
hc 1 1.007941 0.000000 A 2.649533E-01 6.568880E-02
hn 1 1.007941 0.000000 A 1.069078E-01 6.568880E-02
[ moleculetype ]
; name nrexcl
Conformer3D_COMPOUND_CID_2733285 3
; Atomic charges are those loaded from .mol2 file
[ atoms ]
; Index type residue resname atom cgnr charge mass
1 no 1 MOL N 1 0.00000000 14.006703
2 n 1 MOL N 2 0.00000000 14.006703
3 n3 1 MOL N 3 0.00000000 14.006703
4 ca 1 MOL C 4 0.00000000 12.010736
5 ca 1 MOL C 5 0.00000000 12.010736
6 ca 1 MOL C 6 0.00000000 12.010736
7 ca 1 MOL C 7 0.00000000 12.010736
8 ca 1 MOL C 8 0.00000000 12.010736
9 ca 1 MOL C 9 0.00000000 12.010736
10 c 1 MOL C 10 0.00000000 12.010736
11 c3 1 MOL C 11 0.00000000 12.010736
12 c3 1 MOL C 12 0.00000000 12.010736
13 c3 1 MOL C 13 0.00000000 12.010736
14 c3 1 MOL C 14 0.00000000 12.010736
15 c3 1 MOL C 15 0.00000000 12.010736
16 o 1 MOL O 16 0.00000000 15.999405
17 o 1 MOL O 17 0.00000000 15.999405
18 o 1 MOL O 18 0.00000000 15.999405
19 ha 1 MOL H01 19 0.00000000 1.007941
20 ha 1 MOL H02 20 0.00000000 1.007941
21 ha 1 MOL H03 21 0.00000000 1.007941
22 ha 1 MOL H04 22 0.00000000 1.007941
23 h1 1 MOL H05 23 0.00000000 1.007941
24 hc 1 MOL H06 24 0.00000000 1.007941
25 hc 1 MOL H07 25 0.00000000 1.007941
26 hc 1 MOL H08 26 0.00000000 1.007941
27 hc 1 MOL H09 27 0.00000000 1.007941
28 hc 1 MOL H10 28 0.00000000 1.007941
29 hc 1 MOL H11 29 0.00000000 1.007941
30 hc 1 MOL H12 30 0.00000000 1.007941
31 hc 1 MOL H13 31 0.00000000 1.007941
32 hc 1 MOL H14 32 0.00000000 1.007941
33 hn 1 MOL H 33 0.00000000 1.007941
34 hn 1 MOL H 34 0.00000000 1.007941
35 hn 1 MOL H 35 0.00000000 1.007941
[ bonds ]
; atom_i atom_j functype r0 (nm) k (kJ/mol/nm^2)
1 5 1 0.146890 2.691986E+05 ; N-C, prebuilt ca-no
1 16 1 0.122600 6.207382E+05 ; N-O, prebuilt no-o
1 17 1 0.122600 6.207382E+05 ; N-O, prebuilt no-o
2 8 1 0.141210 3.214986E+05 ; N-C, prebuilt ca-n
2 10 1 0.137890 3.578157E+05 ; N-C, prebuilt c-n
2 33 1 0.101290 3.373978E+05 ; N-H, prebuilt hn-n
3 11 1 0.146470 2.727131E+05 ; N-C, prebuilt c3-n3
3 34 1 0.101900 3.283603E+05 ; N-H, prebuilt hn-n3
3 35 1 0.101900 3.283603E+05 ; N-H, prebuilt hn-n3
4 5 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca
4 9 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca
4 19 1 0.108600 2.893654E+05 ; C-H01, prebuilt ca-ha
5 6 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca
6 7 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca
6 20 1 0.108600 2.893654E+05 ; C-H02, prebuilt ca-ha
7 8 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca
7 21 1 0.108600 2.893654E+05 ; C-H03, prebuilt ca-ha
8 9 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca
9 22 1 0.108600 2.893654E+05 ; C-H04, prebuilt ca-ha
10 11 1 0.152410 2.619184E+05 ; C-C, prebuilt c-c3
10 18 1 0.121830 5.336274E+05 ; C-O, prebuilt c-o
11 12 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3
11 23 1 0.109690 2.766461E+05 ; C-H05, prebuilt c3-h1
12 13 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3
12 24 1 0.109690 2.766461E+05 ; C-H06, prebuilt c3-hc
12 25 1 0.109690 2.766461E+05 ; C-H07, prebuilt c3-hc
13 14 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3
13 15 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3
13 26 1 0.109690 2.766461E+05 ; C-H08, prebuilt c3-hc
14 27 1 0.109690 2.766461E+05 ; C-H09, prebuilt c3-hc
14 28 1 0.109690 2.766461E+05 ; C-H10, prebuilt c3-hc
14 29 1 0.109690 2.766461E+05 ; C-H11, prebuilt c3-hc
15 30 1 0.109690 2.766461E+05 ; C-H12, prebuilt c3-hc
15 31 1 0.109690 2.766461E+05 ; C-H13, prebuilt c3-hc
15 32 1 0.109690 2.766461E+05 ; C-H14, prebuilt c3-hc
[ angles ]
; atom_i atom_j atom_k functype a0 (Deg.) k (kJ/mol/rad^2)
5 1 16 1 117.760 5.748816E+02 ; C-N-O, prebuilt ca-no-o
5 1 17 1 117.760 5.748816E+02 ; C-N-O, prebuilt ca-no-o
16 1 17 1 125.080 6.418256E+02 ; O-N-O, prebuilt o-no-o
8 2 10 1 123.710 5.338784E+02 ; C-N-C, prebuilt c-n-ca
8 2 33 1 116.000 3.983168E+02 ; C-N-H, prebuilt ca-n-hn
10 2 33 1 117.550 4.041744E+02 ; C-N-H, prebuilt c-n-hn
11 3 34 1 109.290 3.966432E+02 ; C-N-H, prebuilt c3-n3-hn
11 3 35 1 109.290 3.966432E+02 ; C-N-H, prebuilt c3-n3-hn
34 3 35 1 106.400 3.464352E+02 ; H-N-H, prebuilt hn-n3-hn
5 4 9 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca
5 4 19 1 119.880 4.033376E+02 ; C-C-H01, prebuilt ca-ca-ha
9 4 19 1 119.880 4.033376E+02 ; C-C-H01, prebuilt ca-ca-ha
1 5 4 1 119.010 5.589824E+02 ; N-C-C, prebuilt ca-ca-no
1 5 6 1 119.010 5.589824E+02 ; N-C-C, prebuilt ca-ca-no
4 5 6 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca
5 6 7 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca
5 6 20 1 119.880 4.033376E+02 ; C-C-H02, prebuilt ca-ca-ha
7 6 20 1 119.880 4.033376E+02 ; C-C-H02, prebuilt ca-ca-ha
6 7 8 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca
6 7 21 1 119.880 4.033376E+02 ; C-C-H03, prebuilt ca-ca-ha
8 7 21 1 119.880 4.033376E+02 ; C-C-H03, prebuilt ca-ca-ha
2 8 7 1 120.190 5.681872E+02 ; N-C-C, prebuilt ca-ca-n
2 8 9 1 120.190 5.681872E+02 ; N-C-C, prebuilt ca-ca-n
7 8 9 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca
4 9 8 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca
4 9 22 1 119.880 4.033376E+02 ; C-C-H04, prebuilt ca-ca-ha
8 9 22 1 119.880 4.033376E+02 ; C-C-H04, prebuilt ca-ca-ha
2 10 11 1 115.180 5.589824E+02 ; N-C-C, prebuilt c3-c-n
2 10 18 1 123.050 6.209056E+02 ; N-C-O, prebuilt n-c-o
11 10 18 1 123.200 5.640032E+02 ; C-C-O, prebuilt c3-c-o
3 11 10 1 111.140 5.547984E+02 ; N-C-C, prebuilt c-c3-n3
3 11 12 1 111.040 5.522880E+02 ; N-C-C, prebuilt c3-c3-n3
3 11 23 1 109.880 4.142160E+02 ; N-C-H05, prebuilt h1-c3-n3
10 11 12 1 111.040 5.296944E+02 ; C-C-C, prebuilt c-c3-c3
10 11 23 1 108.220 3.932960E+02 ; C-C-H05, prebuilt c-c3-h1
12 11 23 1 109.560 3.882752E+02 ; C-C-H05, prebuilt c3-c3-h1
11 12 13 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3
11 12 24 1 109.800 3.874384E+02 ; C-C-H06, prebuilt c3-c3-hc
11 12 25 1 109.800 3.874384E+02 ; C-C-H07, prebuilt c3-c3-hc
13 12 24 1 109.800 3.874384E+02 ; C-C-H06, prebuilt c3-c3-hc
13 12 25 1 109.800 3.874384E+02 ; C-C-H07, prebuilt c3-c3-hc
24 12 25 1 107.580 3.296992E+02 ; H06-C-H07, prebuilt hc-c3-hc
12 13 14 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3
12 13 15 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3
12 13 26 1 109.800 3.874384E+02 ; C-C-H08, prebuilt c3-c3-hc
14 13 15 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3
14 13 26 1 109.800 3.874384E+02 ; C-C-H08, prebuilt c3-c3-hc
15 13 26 1 109.800 3.874384E+02 ; C-C-H08, prebuilt c3-c3-hc
13 14 27 1 109.800 3.874384E+02 ; C-C-H09, prebuilt c3-c3-hc
13 14 28 1 109.800 3.874384E+02 ; C-C-H10, prebuilt c3-c3-hc
13 14 29 1 109.800 3.874384E+02 ; C-C-H11, prebuilt c3-c3-hc
27 14 28 1 107.580 3.296992E+02 ; H09-C-H10, prebuilt hc-c3-hc
27 14 29 1 107.580 3.296992E+02 ; H09-C-H11, prebuilt hc-c3-hc
28 14 29 1 107.580 3.296992E+02 ; H10-C-H11, prebuilt hc-c3-hc
13 15 30 1 109.800 3.874384E+02 ; C-C-H12, prebuilt c3-c3-hc
13 15 31 1 109.800 3.874384E+02 ; C-C-H13, prebuilt c3-c3-hc
13 15 32 1 109.800 3.874384E+02 ; C-C-H14, prebuilt c3-c3-hc
30 15 31 1 107.580 3.296992E+02 ; H12-C-H13, prebuilt hc-c3-hc
30 15 32 1 107.580 3.296992E+02 ; H12-C-H14, prebuilt hc-c3-hc
31 15 32 1 107.580 3.296992E+02 ; H13-C-H14, prebuilt hc-c3-hc
[ dihedrals ] ; propers
; atom_i atom_j atom_k atom_l functype d0 (Deg.) k (kJ/mol/rad^2) ; Case of functype=2
; atom_i atom_j atom_k atom_l functype phase (Deg.) kd (kJ/mol) pn ; Case of functype=9
1 5 4 9 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X
1 5 4 19 9 180.000 15.16700 2 ; N-C-C-H01, prebuilt X-ca-ca-X
1 5 6 7 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X
1 5 6 20 9 180.000 15.16700 2 ; N-C-C-H02, prebuilt X-ca-ca-X
2 8 7 6 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X
2 8 7 21 9 180.000 15.16700 2 ; N-C-C-H03, prebuilt X-ca-ca-X
2 8 9 4 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X
2 8 9 22 9 180.000 15.16700 2 ; N-C-C-H04, prebuilt X-ca-ca-X
2 10 11 3 9 180.000 0.00000 2 ; N-C-C-N, prebuilt X-c-c3-X
2 10 11 12 9 0.000 0.41840 4 ; N-C-C-C, prebuilt c3-c3-c-n
2 10 11 12 9 0.000 0.29288 2 ; N-C-C-C, prebuilt c3-c3-c-n
2 10 11 23 9 180.000 0.00000 2 ; N-C-C-H05, prebuilt X-c-c3-X
3 11 10 18 9 180.000 0.00000 2 ; N-C-C-O, prebuilt X-c-c3-X
3 11 12 13 9 0.000 0.65084 3 ; N-C-C-C, prebuilt X-c3-c3-X
3 11 12 24 9 0.000 0.65084 3 ; N-C-C-H06, prebuilt X-c3-c3-X
3 11 12 25 9 0.000 0.65084 3 ; N-C-C-H07, prebuilt X-c3-c3-X
4 5 1 16 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X
4 5 1 17 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X
4 5 6 7 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X
4 5 6 20 9 180.000 15.16700 2 ; C-C-C-H02, prebuilt X-ca-ca-X
4 9 8 7 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X
5 4 9 8 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X
5 4 9 22 9 180.000 15.16700 2 ; C-C-C-H04, prebuilt X-ca-ca-X
5 6 7 8 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X
5 6 7 21 9 180.000 15.16700 2 ; C-C-C-H03, prebuilt X-ca-ca-X
6 5 1 16 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X
6 5 1 17 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X
6 5 4 9 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X
6 5 4 19 9 180.000 15.16700 2 ; C-C-C-H01, prebuilt X-ca-ca-X
6 7 8 9 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X
7 8 2 10 9 180.000 1.88280 2 ; C-C-N-C, prebuilt X-ca-n-X
7 8 2 33 9 180.000 1.88280 2 ; C-C-N-H, prebuilt X-ca-n-X
7 8 9 22 9 180.000 15.16700 2 ; C-C-C-H04, prebuilt X-ca-ca-X
8 2 10 11 9 180.000 10.46000 2 ; C-N-C-C, prebuilt X-c-n-X
8 2 10 18 9 180.000 10.46000 2 ; C-N-C-O, prebuilt X-c-n-X
8 7 6 20 9 180.000 15.16700 2 ; C-C-C-H02, prebuilt X-ca-ca-X
8 9 4 19 9 180.000 15.16700 2 ; C-C-C-H01, prebuilt X-ca-ca-X
9 8 2 10 9 180.000 1.88280 2 ; C-C-N-C, prebuilt X-ca-n-X
9 8 2 33 9 180.000 1.88280 2 ; C-C-N-H, prebuilt X-ca-n-X
9 8 7 21 9 180.000 15.16700 2 ; C-C-C-H03, prebuilt X-ca-ca-X
10 11 3 34 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X
10 11 3 35 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X
10 11 12 13 9 0.000 0.65084 3 ; C-C-C-C, prebuilt X-c3-c3-X
10 11 12 24 9 0.000 0.65084 3 ; C-C-C-H06, prebuilt X-c3-c3-X
10 11 12 25 9 0.000 0.65084 3 ; C-C-C-H07, prebuilt X-c3-c3-X
11 10 2 33 9 180.000 10.46000 2 ; C-C-N-H, prebuilt X-c-n-X
11 12 13 14 9 0.000 0.75312 3 ; C-C-C-C, prebuilt c3-c3-c3-c3
11 12 13 14 9 180.000 1.04600 2 ; C-C-C-C, prebuilt c3-c3-c3-c3
11 12 13 14 9 180.000 0.83680 1 ; C-C-C-C, prebuilt c3-c3-c3-c3
11 12 13 15 9 0.000 0.75312 3 ; C-C-C-C, prebuilt c3-c3-c3-c3
11 12 13 15 9 180.000 1.04600 2 ; C-C-C-C, prebuilt c3-c3-c3-c3
11 12 13 15 9 180.000 0.83680 1 ; C-C-C-C, prebuilt c3-c3-c3-c3
11 12 13 26 9 0.000 0.66944 3 ; C-C-C-H08, prebuilt hc-c3-c3-c3
12 11 3 34 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X
12 11 3 35 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X
12 11 10 18 9 180.000 0.00000 2 ; C-C-C-O, prebuilt X-c-c3-X
12 13 14 27 9 0.000 0.66944 3 ; C-C-C-H09, prebuilt hc-c3-c3-c3
12 13 14 28 9 0.000 0.66944 3 ; C-C-C-H10, prebuilt hc-c3-c3-c3
12 13 14 29 9 0.000 0.66944 3 ; C-C-C-H11, prebuilt hc-c3-c3-c3
12 13 15 30 9 0.000 0.66944 3 ; C-C-C-H12, prebuilt hc-c3-c3-c3
12 13 15 31 9 0.000 0.66944 3 ; C-C-C-H13, prebuilt hc-c3-c3-c3
12 13 15 32 9 0.000 0.66944 3 ; C-C-C-H14, prebuilt hc-c3-c3-c3
13 12 11 23 9 0.000 0.65084 3 ; C-C-C-H05, prebuilt X-c3-c3-X
14 13 12 24 9 0.000 0.66944 3 ; C-C-C-H06, prebuilt hc-c3-c3-c3
14 13 12 25 9 0.000 0.66944 3 ; C-C-C-H07, prebuilt hc-c3-c3-c3
14 13 15 30 9 0.000 0.66944 3 ; C-C-C-H12, prebuilt hc-c3-c3-c3
14 13 15 31 9 0.000 0.66944 3 ; C-C-C-H13, prebuilt hc-c3-c3-c3
14 13 15 32 9 0.000 0.66944 3 ; C-C-C-H14, prebuilt hc-c3-c3-c3
15 13 12 24 9 0.000 0.66944 3 ; C-C-C-H06, prebuilt hc-c3-c3-c3
15 13 12 25 9 0.000 0.66944 3 ; C-C-C-H07, prebuilt hc-c3-c3-c3
15 13 14 27 9 0.000 0.66944 3 ; C-C-C-H09, prebuilt hc-c3-c3-c3
15 13 14 28 9 0.000 0.66944 3 ; C-C-C-H10, prebuilt hc-c3-c3-c3
15 13 14 29 9 0.000 0.66944 3 ; C-C-C-H11, prebuilt hc-c3-c3-c3
18 10 2 33 9 180.000 10.46000 2 ; O-C-N-H, prebuilt hn-n-c-o
18 10 2 33 9 0.000 8.36800 1 ; O-C-N-H, prebuilt hn-n-c-o
18 10 11 23 9 0.000 3.34720 1 ; O-C-C-H05, prebuilt h1-c3-c-o
18 10 11 23 9 0.000 0.00000 2 ; O-C-C-H05, prebuilt h1-c3-c-o
18 10 11 23 9 180.000 0.33472 3 ; O-C-C-H05, prebuilt h1-c3-c-o
19 4 9 22 9 180.000 15.16700 2 ; H01-C-C-H04, prebuilt X-ca-ca-X
20 6 7 21 9 180.000 15.16700 2 ; H02-C-C-H03, prebuilt X-ca-ca-X
23 11 3 34 9 0.000 1.25520 3 ; H05-C-N-H, prebuilt X-c3-n3-X
23 11 3 35 9 0.000 1.25520 3 ; H05-C-N-H, prebuilt X-c3-n3-X
23 11 12 24 9 0.000 0.65084 3 ; H05-C-C-H06, prebuilt X-c3-c3-X
23 11 12 25 9 0.000 0.65084 3 ; H05-C-C-H07, prebuilt X-c3-c3-X
24 12 13 26 9 0.000 0.62760 3 ; H06-C-C-H08, prebuilt hc-c3-c3-hc
25 12 13 26 9 0.000 0.62760 3 ; H07-C-C-H08, prebuilt hc-c3-c3-hc
26 13 14 27 9 0.000 0.62760 3 ; H08-C-C-H09, prebuilt hc-c3-c3-hc
26 13 14 28 9 0.000 0.62760 3 ; H08-C-C-H10, prebuilt hc-c3-c3-hc
26 13 14 29 9 0.000 0.62760 3 ; H08-C-C-H11, prebuilt hc-c3-c3-hc
26 13 15 30 9 0.000 0.62760 3 ; H08-C-C-H12, prebuilt hc-c3-c3-hc
26 13 15 31 9 0.000 0.62760 3 ; H08-C-C-H13, prebuilt hc-c3-c3-hc
26 13 15 32 9 0.000 0.62760 3 ; H08-C-C-H14, prebuilt hc-c3-c3-hc
[ pairs ] ; Yielded based on rotatable dihedrals
; atom_i atom_j functype
1 9 1 ; N-C-C-C
1 19 1 ; N-C-C-H01
1 7 1 ; N-C-C-C
1 20 1 ; N-C-C-H02
2 6 1 ; N-C-C-C
2 21 1 ; N-C-C-H03
2 4 1 ; N-C-C-C
2 22 1 ; N-C-C-H04
2 3 1 ; N-C-C-N
2 12 1 ; N-C-C-C
2 23 1 ; N-C-C-H05
3 18 1 ; N-C-C-O
3 13 1 ; N-C-C-C
3 24 1 ; N-C-C-H06
3 25 1 ; N-C-C-H07
4 16 1 ; C-C-N-O
4 17 1 ; C-C-N-O
4 7 1 ; C-C-C-C
4 20 1 ; C-C-C-H02
5 8 1 ; C-C-C-C
5 22 1 ; C-C-C-H04
5 21 1 ; C-C-C-H03
6 16 1 ; C-C-N-O
6 17 1 ; C-C-N-O
6 9 1 ; C-C-C-C
6 19 1 ; C-C-C-H01
7 10 1 ; C-C-N-C
7 33 1 ; C-C-N-H
7 22 1 ; C-C-C-H04
8 11 1 ; C-N-C-C
8 18 1 ; C-N-C-O
8 20 1 ; C-C-C-H02
8 19 1 ; C-C-C-H01
9 10 1 ; C-C-N-C
9 33 1 ; C-C-N-H
9 21 1 ; C-C-C-H03
10 34 1 ; C-C-N-H
10 35 1 ; C-C-N-H
10 13 1 ; C-C-C-C
10 24 1 ; C-C-C-H06
10 25 1 ; C-C-C-H07
11 33 1 ; C-C-N-H
11 14 1 ; C-C-C-C
11 15 1 ; C-C-C-C
11 26 1 ; C-C-C-H08
12 34 1 ; C-C-N-H
12 35 1 ; C-C-N-H
12 18 1 ; C-C-C-O
12 27 1 ; C-C-C-H09
12 28 1 ; C-C-C-H10
12 29 1 ; C-C-C-H11
12 30 1 ; C-C-C-H12
12 31 1 ; C-C-C-H13
12 32 1 ; C-C-C-H14
13 23 1 ; C-C-C-H05
14 24 1 ; C-C-C-H06
14 25 1 ; C-C-C-H07
14 30 1 ; C-C-C-H12
14 31 1 ; C-C-C-H13
14 32 1 ; C-C-C-H14
15 24 1 ; C-C-C-H06
15 25 1 ; C-C-C-H07
15 27 1 ; C-C-C-H09
15 28 1 ; C-C-C-H10
15 29 1 ; C-C-C-H11
18 33 1 ; O-C-N-H
18 23 1 ; O-C-C-H05
19 22 1 ; H01-C-C-H04
20 21 1 ; H02-C-C-H03
23 34 1 ; H05-C-N-H
23 35 1 ; H05-C-N-H
23 24 1 ; H05-C-C-H06
23 25 1 ; H05-C-C-H07
24 26 1 ; H06-C-C-H08
25 26 1 ; H07-C-C-H08
26 27 1 ; H08-C-C-H09
26 28 1 ; H08-C-C-H10
26 29 1 ; H08-C-C-H11
26 30 1 ; H08-C-C-H12
26 31 1 ; H08-C-C-H13
26 32 1 ; H08-C-C-H14
[ dihedrals ] ; impropers
; atom_i atom_j atom_k atom_l functype phase (Deg.) kd (kJ/mol) pn
8 10 2 33 4 180.000 4.60240 2 ; C-C-N-H, prebuilt X-X-n-hn
5 9 4 19 4 180.000 4.60240 2 ; C-C-C-H01, prebuilt X-X-ca-ha
1 4 5 6 4 180.000 4.60240 2 ; N-C-C-C, guess (same as GAFF X -X -ca-ha)
5 7 6 20 4 180.000 4.60240 2 ; C-C-C-H02, prebuilt X-X-ca-ha
6 8 7 21 4 180.000 4.60240 2 ; C-C-C-H03, prebuilt X-X-ca-ha
2 7 8 9 4 180.000 4.60240 2 ; N-C-C-C, guess (same as GAFF X -X -ca-ha)
4 8 9 22 4 180.000 4.60240 2 ; C-C-C-H04, prebuilt X-X-ca-ha
2 11 10 18 4 180.000 43.93200 2 ; N-C-C-O, prebuilt X-X-c-o

80
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# created with PyMOL 3.0.0
@<TRIPOS>MOLECULE
complex-S112D
35 35 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 N -5.390 2.121 -9.532 N.2 1 UNK1 0.000
2 N -10.664 3.190 -9.419 N.pl3 1 UNK1 0.000
3 N -13.495 1.939 -10.893 N.3 1 UNK1 0.000
4 C -7.068 3.662 -9.763 C.2 1 UNK1 0.000
5 C -6.613 2.369 -9.506 C.2 1 UNK1 0.000
6 C -7.525 1.353 -9.220 C.2 1 UNK1 0.000
7 C -8.891 1.630 -9.190 C.2 1 UNK1 0.000
8 C -9.347 2.923 -9.447 C.2 1 UNK1 0.000
9 C -8.435 3.939 -9.734 C.2 1 UNK1 0.000
10 C -11.408 3.089 -10.564 C.2 1 UNK1 0.000
11 C -12.066 1.780 -10.923 C.3 1 UNK1 0.000
12 C -11.633 1.360 -12.322 C.3 1 UNK1 0.000
13 C -10.441 0.417 -12.222 C.3 1 UNK1 0.000
14 C -9.212 1.086 -12.822 C.3 1 UNK1 0.000
15 C -10.744 -0.866 -12.985 C.3 1 UNK1 0.000
16 O -4.535 3.072 -9.817 O.2 1 UNK1 0.000
17 O -4.961 0.910 -9.274 O.2 1 UNK1 0.000
18 O -11.537 4.049 -11.287 O.2 1 UNK1 0.000
19 H01 -6.356 4.456 -9.987 H 1 UNK1 0.000
20 H02 -7.170 0.342 -9.020 H 1 UNK1 0.000
21 H03 -9.603 0.836 -8.966 H 1 UNK1 0.000
22 H04 -8.791 4.949 -9.936 H 1 UNK1 0.000
23 H05 -11.769 1.015 -10.205 H 1 UNK1 0.000
24 H06 -11.351 2.243 -12.896 H 1 UNK1 0.000
25 H07 -12.458 0.852 -12.822 H 1 UNK1 0.000
26 H08 -10.251 0.181 -11.175 H 1 UNK1 0.000
27 H09 -8.372 0.391 -12.797 H 1 UNK1 0.000
28 H10 -9.419 1.369 -13.854 H 1 UNK1 0.000
29 H11 -8.963 1.976 -12.244 H 1 UNK1 0.000
30 H12 -11.619 -0.714 -13.617 H 1 UNK1 0.000
31 H13 -9.889 -1.130 -13.607 H 1 UNK1 0.000
32 H14 -10.942 -1.672 -12.278 H 1 UNK1 0.000
33 H -11.107 3.466 -8.551 H 1 UNK1 0.000
34 H -13.775 2.330 -9.994 H 1 UNK1 0.000
35 H -13.774 2.642 -11.577 H 1 UNK1 0.000
@<TRIPOS>BOND
1 1 5 1
2 1 16 ar
3 1 17 ar
4 2 8 1
5 2 10 1
6 2 33 1
7 3 11 1
8 3 34 1
9 3 35 1
10 4 5 ar
11 4 9 ar
12 4 19 1
13 5 6 ar
14 6 7 ar
15 6 20 1
16 7 8 ar
17 7 21 1
18 8 9 ar
19 9 22 1
20 10 11 1
21 10 18 2
22 11 12 1
23 11 23 1
24 12 13 1
25 12 24 1
26 12 25 1
27 13 14 1
28 13 15 1
29 13 26 1
30 14 27 1
31 14 28 1
32 14 29 1
33 15 30 1
34 15 31 1
35 15 32 1
@<TRIPOS>SUBSTRUCTURE
1 UNK1 1 GROUP 1 L_Le UNK

14
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; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev5) on 2024-09-19
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
#include "Conformer3D_COMPOUND_CID_2733285.itp"
[ system ]
Conformer3D_COMPOUND_CID_2733285
[ molecules ]
; Molecule nmols
Conformer3D_COMPOUND_CID_2733285 1

7449
script/S112D/protein.pdb Normal file
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