[gmx-users] cnvtop in GROMOS96

[Daan Virtual]

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
> ___________________________________________
>
>
>


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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