On 8/15/12 9:12 AM, Ankita naithani wrote:
Is this because the topol_Protein_Chain_D.itp has a line of including
the position restraint file for chain D?
Yes, #include statements for position restraint files are contained in each
chain topology.
-Justin
On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani
<ankitanaith...@gmail.com> wrote:
Hi,
I noticed that in my topology file, there is no inclusion of position
restraint file for my protein. For instance, my topology file looks
like this:
; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_E.itp"
#include "topol_Protein_chain_F.itp"
#include "topol_Protein_chain_G.itp"
;Include ligand topology
#include "FDP_Dp.itp"
; Include water topology
#include "gromos53a6.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos53a6.ff/ions.itp"
But, after running pdb2gmx, I do get 4 posre files for all the
individual chains. Do I need to add in them manually? Also, I am
unable to understand as to why did it not get included in the first
instance itself? I am using gromos53a6 force field.
Best Wishes,
--
Ankita Naithani
--
========================================
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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