[gmx-users] em ok, md wrong

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 29 01:19:53 CET 2009

Yuri Garmay wrote:
> 2009/10/28 Liliya Shamova <lshamova at yahoo.com <mailto:lshamova at yahoo.com>>
>     Hi everybody!
> Dihedrals seem be incorrect. Check it. (I don't know what have to be, is 
> it planar molecule or not, it have be known, but it seems to be 
> incorrect, as you say molecule distorted) Additionally, you should use 
> improper dihedrals for making planar parts.

Indeed, the dihedrals don't make much sense.  Based on ASPH, you should define a 
HO-OH-C-O dihedral for each carboxylic acid group, and I would think you would 
also need to define an O-C-C-O torsion.  All of this information is in the 
ffoplsaabon.itp and ffoplsaa.rtp files.  You should definitely define impropers 
to keep the carboxylic acid groups planar.  Using the ASPH entry in ffoplsaa.rtp 
is a good start.  If hydrogens are collapsing into neighboring acid groups, your 
[pairs] directive is probably incorrect.

> P.S.
> 1) I think, this acid is charged in neutral pH. OOC-COO (2-), not HOOC-COOH

True, but this is (as described) a vacuum simulation, so we're not dealing with 
solution pH.


> 2) Why not to use topology of charged ASP residue side chaas starting point?
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list