[gmx-users] Generation of the Distance Restraints

[James Starlight]

Francesca,

Yes I suppose this is good aproach for the generation of position
restricktions on the desired atoms. But I want to restrain the distance
between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two
different residues).

Also I want to restrain some dihedral angles in the desired rotameric forms.

In literature I've found that peple have dome the same things in Gromacs
but I could not find detailed algorithm of such methodology :(

James

12 марта 2012 г. 18:05 пользователь francesca vitalini <
francesca.vitalini11 at gmail.com> написал:

> I think you can make an index file using make_ndx where you specify
> the atoms you want to restraint.
> Hope this can help.
> Francesca
>
> 2012/3/12 James Starlight <jmsstarlight at gmail.com>:
> > Dear Gromacs users!
> >
> >
> > I want to perform constrained MD simulation of my protein with inclusion
> of
> > some experimental restraints.
> >
> >
> > 1) I found that genrest cpmmand could be usefull for the generation of
> the
> > distance restrictions wich I could use in my constrined simulation.
> >
> > Also in manual I've found that command like
> >
> > genrestr -f b2ar.gro -disre -index.ndx -o test.itp
> >
> > will produce some distance restricted matrix of the whole groups
> presented
> > in the index.ndx file.
> >
> > So how I could select to contrain selected residues within selected
> distance
> > by means the index file?  E.g I've manually point out 2 residues in
> > index.ndx. I waant to preserve between that residues some desired
> distance D
> > wich I've obtaine from the experimental data. How I could do it via
> genrestr
> > and waht addition flags should I use for that purpose ?
> >
> >
> > 2) Is there any way to apply gradually the desired dist.resrs during
> MDrun
> > to prevent some artifacts in my system wich would occur due to the rapid
> > application of the dis.res ( e.g in cases where the conformation of the
> > started structure and that wich I'd obtained fter application of the
> > restrains are slightly different)?
> >
> > Thanks for help,
> >
> >
> > James
> >
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