On 30/03/2012 8:39 AM, francesca vitalini wrote:
Thank you Justin for your answer. I'm trying to add the position
restraints to my protein, but I have a problem. My topology is made of
a chain repeated twice and if I want to build the position restraints
through genrestr from a gro file, the numeration of the atoms would
put the 2 chains sequentially one after the other, but then the index
would be out of bounds;
As genrestr -h and the manual tells you (and as was discussed on this
list a day or two ago), [position_restraints] apply to all copies of
that [moleculetype]. So use genrestr on the first molecule only and you
will have position restraints for both molecules for the price of one.
if I try to generate the topology from x2top
it has been taking more than 6 hours and hasn't finish yet. If instead
I try to use the posre.itp built from pdb2gmx I still have the LINCS
warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas
on a faster way to add my position restraints or how to solve the
LINCS error? Thank you very much.
Follow the advice here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
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