[gmx-users] NADP topology

[Anton Feenstra]

From: Sergio Manzetti <sergio.manzetti at bio.uio.no>
> 
> Dear GMX users, I understand that the NAD topology is present in the 
> Gromos force fields, but I need the topology of NADP . Given that HETATM 
> abbreviations are tri-leteral, does anyone know what the trilerteral 
> code of NADP is in the library? I have no acces  to this library from 
> here, that is why I ask.

It's in the GromOS manual: NADP, NADH, NDPH, NDPP, NDPHN, for
NAD+ (-1), NADH (-2), NADPH (-3), NADP+ (-2) and NADPH (0) respectively
(numbers in brackets are total charge). What abbreviation(s) would
be used in .pdb files, AFAIK is entirely up to the one who wrote the
.pdb file. (PDB is not a nice, nor a well-designed file format, it is
simply the most used.)

> (Besides I woiuld like to use the OPLS-AA force field) is the 
> nomenclature equal there as well?

That would actually surprise me - my guess is, no, not equal.
Probably both building blocks as well as atoms have different names.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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