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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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