[gmx-users] GROMOS96 topology

[Daan Virtual]

Hi Ruben

The problem here is that for historical reasons GROMOS87 is limited to a
maximum of 99 atoms, bonds, angles etc. This is simply because there is
only a two-character space for these parameters in the topology.
Therefore, originally PRODRG could also only deal with < 100 atoms. This
limitation has now been removed but it does mean that the GROMOS87 output
produced with > 100 atoms (or indeed > 100 bonds, angles etc.) contains
rubbish (the ** in your file). This problem as such cannot be solved.

However, I am quite willing to incorporate GROMOS96 format in PRODRG
directly if somebody on this list con provide me with a full set of
installation files and a manual.

cheers

Daan

On Wed, 11 Sep 2002, Ruben Martinez Buey wrote:

> Hi all,
> I have a small molecule with more than 100 atoms/bonds/angles. When
> PRODRG generates the GROMOS87 topology, an error occurs:
> _____________________________
> 29
> DRG
> 6672**3038 0 0 1 1 1 1
> ______________________________________________________________________
>
> I want to use GROMOS96, so I would like to generate a molecular topology
> for GROMOS87 with PRODRG
> and convert to GROMOS96 with the program "cnvtop.64" included in the
> GROMOS96 software.
> Can anyone help me?
> Thanks a lot for your help
> with best regards
> Ruben
> ___________________________________________
>
> Rubén Martínez-Buey. PhD student
> Protein Function and Structure Dept. Lab. 352
> Centro de Investigaciones Biológicas (CIB-CSIC)
> C/ Velázquez, 144  28006  MADRID
> Tlf: +34-91-561 18 00 ext. 4380
> ___________________________________________
>
>
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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

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