[gmx-users] GROMOS96 topology

[David van der Spoel]

On Thu, 2002-09-12 at 22:46, Ruben Martinez Buey wrote:
> 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.
if it minimizes well in gromos87 force field, but not in g96 there mst
likely is an error in your topology


> 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
> ___________________________________________
> 
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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