[gmx-users] D-Serine rtp

[Anton Feenstra]

samantha at biop.ox.ac.uk wrote:

> Hi,
> Another new gromacs user here.
> Does anyone out there have a topology for D-Serine, D-cycloserine or
> 5,7-dichlorokynurenic acid?
> I am about to attempt to create these and hoped some kind soul might
> save me the trouble.

D-serine is trivial: take L-serine and swap the improper on the Ca.

> If not, does anyone have any advice on determining bond angles etc for
> new molecules?

Build yourself 'by analogy', i.e. by looking at similar parts of other
building blocks. Or use the ProDrg webserver, which usually does a good
job in automating this arduous task. You do want to check the generated
topology carefully (as you would for any generated topology), and if
you want the Gromos or OPLS forcefields, you will have to translate it
afterwards (ProDrg only generates Gromacs ff topologies).

If all you have is C, N, H, O and some P or S, it shouldn't be too hard...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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