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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
