[gmx-users] RE: Position restraints

Justin Lemkul jalemkul at vt.edu
Wed Apr 3 12:59:44 CEST 2013

On 4/3/13 2:36 AM, alex rayevsky wrote:
> Thank you for responce and explanation!
> So is it a good alghorithm to use gromacs genrestr command and then
> include this posre.itp file into topology (without any changes) after
> insertion of a ligand.itp?

As long as you use a suitable input file for genrestr, e.g. the ligand only. 
Numbering in the position restraint .itp file is based on [moleculetype], so if 
you use a coordinate file that has multiple molecules in it when running 
genrestr, it won't work.


> Thank you in advance
> On 4/2/13 6:07 AM, alex rayevsky wrote:
> Dear All!
> I have a doubt about the rightness of ligand/molecule integration in the
> topology file. I'm using an amber (tleap) or swissparam.ch to build a
> topology of the residue (modified trna). Is it neccessary to generate a
> position restrain file (genrestr program) for this residue or not? I've
> started both dynamics with/without posrestraints on my residue, however I'm
> really not sure that my results from both of them are different. But I want
> to do everything in right way, so what can you say about this?
> Restraints during equilibration are used to prevent unnatural forces from
> theunequilibrated solvent and help prevent deformation of the structure.
> It's never a bad idea to restrain the whole solute. If I were reading a
> paper thatdescribed restraining the whole solute, except for one residue
> because it wasspecial or difficult to deal with, I would immediately be
> suspicious.
> -Justin


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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