[gmx-users] connecting two chains

Somayeh Alimohammadi somayeh.alimohamadi at gmail.com
Sun Nov 2 11:02:44 CET 2014

Dear gmx users
I am performing a simulation protein- ligand by gromacs.
this protein contain two chains (A & B) which separated from eachother.

 I did the following steps for  pdb file

1- pdb2gmx  –ignh  –f initial.pdb  –o initial.pdb  –p topol.top  -ter

2- editconf -bt cubic –f initial.pdb –o initial.pdb -c –d 0.9

3- genbox  –cp initial.pdb   –cs spc216.gro  –o initial-box.pdb  –p

4- grompp  –f em.mdp  –c initialbox.pdb  –p topol.top  –o xion.tpr

5- genion  -s xion.tpr  -o initial_ions.gro  -p topol.top   -pname NA
 -nname CL  -nn (number of charge)

everything was perfect, but the final pdb file has a problem which

two chains are  connected eachother.
I would like to know how to solve these problems?


Somayeh Alimohammadi
Ph.D Student of Medical Nanotechnology
 Shahid Beheshti University of Medical Sciences

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