[gmx-users] ATP

[Daan van Aalten]

Hi Kay

You can add your hydrogens using the PRODRG server
http://davapc1.bioch.dundee.ac.uk

which will in fact EM your molecule in GMX.

Daan

On Fri, 20 Jun 2003, Kay Gottschalk wrote:

> Hi there,
>
> my system is a protein with ATP, and I'm using the Gromacs ff. In the
> initial pdb-file, 3 hydrogens are missing, thus Gromacs nicely
> complains about that. If I just leave them out (with the '-missing'
> option), ATP is too negatively charged. Is there any reasonable way to
> build the hydrogens with Gromacs? Unfortunately I don't have Insight
> here, and SwissPDB cannot do it. Alternatively I might increase the
> radius and weight and decrease the charge of the affected oxygens in
> the sense of a 'united atoms ATP', but I'd rather avoid that (the
> dipoles just would be fucked up, and h-bonds will not be able to
> form... ). Help would be appreciated.
>
> Thanks a lot,
> Kay.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


##############################################################################

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