Yuri Garmay wrote:
2009/10/28 Liliya Shamova <[email protected] <mailto:[email protected]>>
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.
-Justin
2) Why not to use topology of charged ASP residue side chaas starting point?
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
