On 5/16/15 8:13 AM, Ming Tang wrote:
Dear all,
I want to minimize my system to relax the solvent with the positions of heavy
atoms within the protein restrained. I searched the archives and got the idea
that I need to put something like this in topology:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
But I still have no idea how to get the heavy atoms restrained. Could anybody
tell me how to do this?
pdb2gmx does this automatically for you. It writes posre.itp, which specifies
heavy atom restraints. It's controlled by a similar #ifdef block.
I want to use gromos54a7 ff to simulate my collagen. As Justin suggested, I need to study
the original paper "Definition and testing of the GROMOS force-field versions 54A7
and 54B7" to write my .mdp file. In the paper it says,
1. Each system was energy minimised to relax the solvent with the
positions of the heavy atoms within the protein and RNA restrained.
2. All solute atom positions were restrained to their positions in the
initial structure through a harmonic potential energy term with force constant
of 2.5 9 104 kJ mol-1 nm-2.
Could anybody tell me how to restrain the heavy atoms of protein, and how to
get the solute atom positions restrained with a harmonic potential energy term
with a certain constant?
This is what posre.itp does.
Also note that you don't necessarily have to follow that protocol exactly; my
general advice for proper use of force fields is about proper nonbonded setup.
Preparation of a system often depends on what the system is and if there are any
special considerations. For a simple protein system, it's pretty hard to break
things. I don't see much benefit in restraining atoms during minimization, though.
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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