[gmx-users] em ok, md wrong

[Justin A. Lemkul]

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.

-Justin

> 
> 2) Why not to use topology of charged ASP residue side chaas starting point?
> 
> 
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-- 
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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

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