[gmx-users] connecting two chains

Justin Lemkul jalemkul at vt.edu
Sun Nov 2 13:08:13 CET 2014

On 11/2/14 5:02 AM, Somayeh Alimohammadi wrote:
> 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
> topol.top
> 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?

If the two chains have unique chain identifiers in the starting .pdb file, and 
you don't use pdb2gmx -merge to create any sort of inter-molecular disulfides or 
anything, the chains are not connected.  If there are "bonds" showing up in VMD 
or something, those usually aren't real because VMD isn't always smart.  If 
there is something else going on, please provide evidence of what you mean 
(topology output or whatever else).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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