[gmx-users] How to get the all atom topology file for smallmolecule?

[Anton Feenstra]

Yuhua Song wrote:
> Could I get some hints for manually getting the all atom topology based on
> united atom topology? or I could not try to get all atom topology based on
> united atom topology?  or I can borror some parameter from the existing
> force field?

If you are well enough comfortable with the gromacs topology file formats,
you could try converting your (prodrg) .itp file into an .rtp entry, and
write a corresponding entry in the .hdb. You'd have to add the hydrogens
to the .rtp entry manually (adding bonds, mainly, which isn't too much
work), but with the .hdb entry pdb2gmx will add the hydrogens at the right
position in your molecule structure. If this doesn't make sense to you,
you probably don't want to try... ;-)

-- 
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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