[gmx-users] NADPH topology continued..

[Anton Feenstra]

Sergio Manzetti wrote:
> Dear Anton, I saw that your thesis included also a thorough study on FAD 
> and NADP topologies. In this regard, I'd like to ask you about the 
> problem that now has arisen. After renaming NADPH molecule in the PDB 
> file from NAP tto NADH, the GMX and GROMOS force field recognize 
> obviously the molecule, but not the atomic nomenclature......
> At this stage, I tried to use the atomic nomencalture from the PRODREG 
> server, but it all became so messy I had to abort that attempt.
> 
> What can I do to find the right atomic nomenclature?

Look in the appropriate .rtp file, it's all there.
For 'gromos', you need ffG43a1.rtp (e.g. $GMXDATA/top/ffG43a1.rtp).
Look for a block named '[ NADH ]', the first section is ' [ atoms ]'.
First entry on the line is atom name, then follows atom type.
There is no other option but to re-name all atoms in your .pdb to
the respective names from the .rtp file entry.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | 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)                               |
|_____________|_______________________________________________________|