[gmx-users] PRODRG warning

[Daan van Aalten]

Hi Andrew

Thanks for this not very constructive warning.
It might be useful to tell us what ligand you tried to put in, and most
importantly what forcefield you trie dto use it with. It has been
mentioned pretty explicitly everywhere that *ONLY* the "old" ffgmx
forcefield will work. Other people's tests seem (as far as I am aware) to
indicate that GMX topologies straight out of PRODRG seem to work
reasonably well, although there appears to be some confusion regarding
kJ/kcal units.
So send me your ligand, and I'd be happy to look at it.

cheers

Daan



On Wed, 16 Jan 2002, Andrew Horsfield wrote:

> Hi,
> 
> Maybe I was just being dense, but I have wasted a great deal of time from
> using a topology file from PRODRG. The topology is fine, but the force
> field parameters it introduces give nonsense geometries. By deleting these
> parameters, and just allowing gromacs to use its own parameters, all has
> become well again. Maybe this is obvious to everyone else, but if not,
> then I hope this warning will save you much trouble.
> 
> Cheers,
> 
> Andrew
> 
>   +----------------------------------------------------+
>    Andrew Horsfield       e-mail: horsfield at fecit.co.uk 
>     FECIT, Hayes Park Central, Hayes End Road, Hayes,
>            Middlesex UB4 8FE, United Kingdom.           
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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!
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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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