[gmx-users] GROMOS96 topology

[David van der Spoel]

On Thu, 2002-09-12 at 23:06, Ruben Martinez Buey wrote:
> Hi,
> Thanks alot for your e-mail. Anyway,
> I cannot minimize it in GROMOS87, because it has more than 100 atoms/bonds/angles, and
> this is not supported in G87.
you mean on the prodrg server...

you might try building your molecule using molden or so.
topology is a problem if prodrg doesn't work for you. However, didn't
Daan say that he could no go up until 300 atoms?


> 
> Cheers,
> Ruben
> 
> David van der Spoel wrote:
> 
> > 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
> > > > > ___________________________________________
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > gmx-users mailing list
> > > > > gmx-users at gromacs.org
> > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > >
> > > >
> > > > ##############################################################################
> > > >
> > > > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> --
> ___________________________________________
> 
> 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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