[gmx-users] D-form amino acids

[Daan van Aalten]

Hi

Why worry? As long as you have submitted your entire hexapeptide as one
molecule and the topology is right it does not matter that your
molecule is called UNK ?

Daan

On Wed, 28 May 2003, Regina R. Monaco, Ph.D. wrote:

> HI All-
>
> 	I am trying to submit a calculation to GROMACS on a hexapeptide
> composed of D-form amino acids. My input structure file is in the  .mol
> file format, which I cannot get any program to recognize as being
> composed of anything other than "UNK" residues. I have tried the
> (awesome) PRODRG2 (davapc1.bioch.dundee.ac.uk/prodrg/) site, but the
> .TOP and .ITP output files it generates still have all the residues
> labelled as "UNK".
>
> 	Does anyone know how I can handle this and run an MD simulation?
>
> Thanks,
> Regina Monaco
>
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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