[gmx-users] modeling unnatural amino acids

[Daan van Aalten]

Hi Rich

If it's a small peptide (< 30 amino acids or so) you can try the PRODRG
server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html)

cheers

Daan

On Mon, 22 Apr 2002, Rich McClellan wrote:

> Hi,
>
> I have a peptide composed of unnatural amino acids that I'd like to
> model with GROMACS.  GROMACS (pdb2gmx) is unable to calculate the
> molecular topology of the system and gives an error message stating that
> the residue is not found in the topology database.
>
> Generating the topology file from hand looks daunting so I was wondering
> if somebody has developed a topology database of "other" amino acids or
> have suggestions on the best way to proceed.
>
> 		thanks in advance,
> 		Rich
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust RCD 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