[gmx-users] could all-atom small molecule work with united atom biomemrane?

[Anton Feenstra]

Yuhua Song wrote:

> Dear Gromacs-mailing list and developer:
> 
> I am using the united atom force field ffgmx that addionally add some
> biomembrane information ( got from Gromacs mailing list) to study
> biomembrane, now, I intend to add an all-atom small molecule into the
> system.  I had got many suggestion from mailing list about how to get the
> all atom topology of small molecule using PDB2GMX using OPLSA force field.
> 
> I am wondering that if I get all atom topology of small molecule with
> PDB2GMX using OPLSA force field, could the all atom small molecule work
> together with the united atom Biomembrane which use ffgmx united atom force
> field?  Because the ffgmx and oplsa has different *.atp, *.rtp definition,
> the all atom topology of small molecule from oplsa, the united atom topology
> of biomembrance from ffgmx will get into "doest not match" somehow?

You cannot get a topology of most 'small molecules' using pdb2gmx. It is
usefull mostly for proteins and DNA (i.e. biopolymers). You could use the
ProDrg webserver instead (search list archives, or Google, for ProDrg).


-- 
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/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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