On 6/16/12 6:29 AM, delara aghaie wrote:
Dear Mark
Again some questions:
------------------------------------------
I used -chainsep option to pdb2gmx and generated topology files for two protein
chains and also .gro file containing both chains
........................................
The energy minimization was done successfully and I got average pot.
energy=-1.2*10^6
Then I started NVT simulation for 200 ps with position restraints on proteins.
1)) having the following line in .mdp file will do position restraints on both
chains, considering that each chan has its own .top file????
Yes, it does. Position restraints are applied per [moleculetype], as indicated
in the topology.
define = -DPOSRES ; position restrain the protein
---------------------------------
200 ps, NVT simulation finished, but I think there is something wrong here. This
is part of my nvt.mdp file:
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in
K
As here my protein has two chains, is it necessary to increase the tc-groups???
No. See the following:
http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do
-Justin
I mean should I use for example
tc-grps = Protein_chain_A Protein_chain_B SOl NA (These are the names that
are present at the end of topol.top file)
Thanks
Regards
D.M
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Saturday, 16 June 2012, 12:15
*Subject:* Re: [gmx-users] simulating dimer proteins
On 16/06/2012 5:31 PM, delara aghaie wrote:
Dear Gromacs Users
Running pdb2gmx on a pdb file containing a dimer protein, I used option ((
chainsep id_or_ter)))
This resulted in separated topologies for each chain and separated posre
files. Also in the .gro file, the aminoacides of the second chain started from
number 1. (Without this option the second chain aminoacides will receive
numbers in continuation of numbers of first chain))....
Now:
Can I use these files to continue the simulations or again it is necessary to
follow the procedure explained in multiple chains gromacs???
By definition of pdb2gmx function, you now have a topology and a coordinate file
that matches. That is the minimum requirement for grompp to succeed later.
grompp doesn't care about some aspects of atom numbering - including your
observation above.
Mark
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========================================
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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