[gmx-users] GROMOS96 topology

[Ruben Martinez Buey]

Hi,
Anyway, when I get the GROMOS87 topology, transform by hand to GROMOS96 using the
interaction function parameters of both 87 and 96, and I run a short energy
minimization (with GROMOS96) only with the small molecule, a SHAKE error occurs.
If I switch off SHAKE, anormal bonds are generated after the energy minimization.

Thanks a lot
Cheers,

Ruben


Daan Virtual wrote:

> 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
>
>         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

--
___________________________________________

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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