[gmx-users] NADPH topology continued..

[Daan Virtual]

... or, if you're lazy, run it through PRODRG.

Daan


On Wed, 19 Mar 2003, Anton Feenstra wrote:

> 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)                               |
> |_____________|_______________________________________________________|
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O