[gmx-users] PRODRG topology server problem!

[Daan Virtual]

Dear Chen

Unfortunately PRODRG only works with the implicit atom model for apolar
hydrogens (as in the original GROMOS87 and the first GROMACS force field).
If you don;t want to make a topology for your large molecule you could
just switch to ffgmx - I don;t think there is evidence this is a "very
bad" force field.

cheers

Daan

On 23 Sep 2002 pqchen at eyou.com wrote:

> Dear all:
>   I am a student of Nankai University in China!
>   Recently I want to use gromacs program to study calix[4]pyrrole molecule!But
> when I use the PRODRG topology server to generate the .top file,there is a
> error ocur!The program file can't add the exatly hydrogens to my molecule!In
> the gromacs .top file,there is none of the hydrogens.And my molecule + added
> hydrogens
> show that the hydrogens on the Nitron is absent.Can somebody can help me!
>   BTW:Can gromacs program use other solvents except the water solvent?
>                                                              sincerely yours
>
>                                                              Chen PeiQuan
>
>
>
>
>
> --http://www.eyou.com
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>
>
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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!
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
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