[gmx-users] Re: cnvtop in GROMOS96

[Ruben Martinez Buey]

Daan Virtual wrote:

Dear Daan,
Thanks a lot for your reply,
Anyway, that does not seem the problem. The building block was generated by
PRODRG and contain less than 99 atoms, bonds, bond angles, dihedrals and improper
dihedrals.
Thanks again
with best wishes,
Ruben

> Ruben
>
> Does your molecule (+ H's !!) contain > 99 atoms, bonds, bond angles etc?
>
> GROMOS 87 cannot deal with topology building blocks with any of these
> properties > 99. You can see this quite easily by scanning the topology
> building block for **
>
> cheers
>
> Daan
>
> On Sat, 23 Nov 2002, Ruben Martinez Buey wrote:
>
> > Hi everybody,
> > Does anybody why GROMOS96 lead to this error when I try to run cnvtop,
> > where topology.g87 is a topology for GROMOS87 generated by PRODRG
> >
> > This is the script:
> > rm -f fort.*
> > #---input units
> > ln -s     topology.g87              fort.40    # molecular topology
> >
> > #----output units
> > ln -s     topology.g96              fort.20    # final coordinates
> >
> > #---run the program
> > /usr/local/gromos96/cnvtop.64
> >
> > and this is the result of cnvtop.64:
> >
> >  Scotty's CNVTOP Program!
> >  $Id: cnvtop.f,v 1.15 1996/10/10 16:43:15 wscott Exp $
> >  CNVTOP expects a binary GROMOS87 topology file on
> >  unit 40.
> >  It writes a GROMOS96 topology file to unit 20.
> >  ORDTOP: Error reading NRATT!
> >
> > Thanks in advance,
> > Cheers
> > 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
> > ___________________________________________
> >
> >
> >
>
> ##############################################################################
>
> 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
>
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--
___________________________________________

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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