命令如下：gmx genion –s ions.tpr –o dppc_mg.gro –p system.top –pname MG –conc 0.15 ...
1.1. 创建拓扑与坐标文件 gmxeditconf- 编辑模拟盒子以及写入子组(subgroups) gmxprotonate- 结构质子化 gmxx2top- 根据坐标生成原始拓扑文件 gmxsolvate - 体系溶剂化 gmxinsert-molecules- 将分子插入已有空位 gmxgenconf- 增加”随机”取向的构象 gmxgenion - 在能量有利位置加入单原子离子 gmxgenrestr- 生成索引...
Q: gmx genion命令：往溶剂中添加离子时报错："No line with moleculetype SOL found the [ molecules ] section of file "topol.top"A: 首先检查拓扑文件是否正确，如果在拓扑没有问题的情况下依然报错，往往可能是由于拓扑文件在Windows系统下处理过，行尾标记有问题。用dos2unix工具处理一下拓扑文件...
Q: gmx genion命令:往溶剂中添加离子时报错:"No line with moleculetype SOL found the [ molecules ] section of file "topol.top" A: 首先检查拓扑文件是否正确,如果在拓扑没有问题的情况下依然报错,往往可能是由于拓扑文件在Windows系统下处理过,行尾标记有问题。用dos2unix工具处理一下拓扑文件即可。 2018.11...
gmxgenion-sprotein-water.tpr-oprotein-solvated.gro-conc0.15-neutral-pname NA+-nnameCL- 注意: 为中和体系电荷而添加的离子的数量. 通过将一些水分子替换为离子, 体系的拓扑文件protein.top不再正确. 你可以修改拓扑文件, 减少溶剂分子的数目, 同时在文件的最后一部分(molecules)中SOL的后面增加一行, 指定添加...
各位大佬，我用gmx genion“gmx genion –s mixmem.tpr -o mixmem-solvated.gro–conc 0.15 –...
vi em1.log 8 Add ions to neutralize the system cp em1.mdp ion.mdp grompp -f ion.mdp -c fbp_em1.gro -p fbp.top -o ion.tpr -po -v -nice 0 genion -s ion.tpr -o fbp_ion.gro -g ion.log -np 7 -pname NA -nice 0 Add ions by replacing solvent After that, you need to...
int gmx_genion(int argc, char *argv[]){static char *desc[] = {"genion replaces solvent molecules by monoatomic ions at","the position of the first atoms with the most favorable electrostatic","potential or at random. The potential is calculated on all atoms, using","normal GROMACS ...
above. This .itp was generated after I ran genion on a previous, less interesting system, then ran pdb2gmx over again which built the .itp below. Unfortunately, running pdb2gmx in the present case would be a bit of a pain, since I'm using GAFF parameters for ...
> and Ions by genion. > the above result is for Energy minimization after adding ions by genion. > > I did what you said.but when I was generating NPT equilibration > I recieved this massage: > > > Step 0, time 0 (ps) LINCS WARNING ...