R: [gmx-users] Dihedral restraints
A.STEVENAZZI at italfarmaco.com
Wed Mar 15 16:49:24 CET 2006
I did check the mailing list archives and could not find anything
Moreover, I have experienced some problems with version 3.3 of Gromacs
related to PME (see the mailing list archives) and I was forced to
install the 3.2.1 version in order to run a simulation.
So you are telling me that dihedral restraints can not be set up in the
I beg you pardon if these are stupid questions, but I have started to
use Gromacs just 2 weeks ago.
STEVENAZZI ANDREA wrote:
> Dear Gromacs Users
> I am trying to use Gromacs for the MD of a small modified peptide
> 4 residues with one ethylated) and I would like to set up one dihedral
> restraint in the topology file.
> I have not found anything useful on the paper manual regarding
> restraints and thought that it might not be possible to set them.
> However, analysing the mdout.mdp file I realised that the keyword
> (dihedral angle restraints) is actually there and can be turned on.
> If that is true, does anybody know the right lines to insert in the
> topology file in order to set properly a dihedral restraints?
manual is a bit outdated. check mailing list archives. it is possible
> Best regards
> Andrea Stevenazzi
> Medicinal & Computer Chemistry
> Italfarmaco Research Centre
> Italfarmaco SpA
> Via dei Lavoratori 54
> 20092 Cinisello Balsamo
> E-mail: a.stevenazzi at italfarmaco.com
<mailto:a.stevenazzi at italfarmaco.com>
> Tel: +39-02-64433097
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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