[gmx-users] multiple chain restrain problem

Justin Lemkul jalemkul at vt.edu
Thu Jun 27 13:50:50 CEST 2013

On 6/27/13 6:27 AM, Albert wrote:
> Hello:
>   I've got two protein chain in my system. I generate gmx.pdb by pb2gmx, and
> gromacs generate toplogy and restrain file for each chain:
> gmx.pdb
>   topol_chain_A.itp
> topol_chain_B.itp
> porschain_A.itp
> porschain_B.itp
> I noticed that the gmx.pdb doesn't contain any chain information. I am going to
> equilibrate the system first restrain the heavy atoms which can be specified by
> porschain_A.itp and porschain_B.itp. However, in the next step I am going to
> restrain only the backbone of chain A, how can we to do this? The chain
> information in new generated gmx.pdb lost.... When I use command:
> genrestr -f gmx.pdb -p porsB
> it doesn't contains selection for chain....

Then select by residue number.  Note that genrestr will only work for the first 
molecule, since position restraint numbering is based on the [moleculetype] 
numbering, not the coordinate file numbering.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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