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Daan Virtual wrote:
<p>Dear Daan,
<br>Thanks a lot for your reply,
<br>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.
<br>Thanks again
<br>with best wishes,
<br>Ruben
<blockquote TYPE=CITE>Ruben
<p>Does your molecule (+ H's !!) contain > 99 atoms, bonds, bond angles
etc?
<p>GROMOS 87 cannot deal with topology building blocks with any of these
<br>properties > 99. You can see this quite easily by scanning the topology
<br>building block for **
<p>cheers
<p>Daan
<p>On Sat, 23 Nov 2002, Ruben Martinez Buey wrote:
<p>> Hi everybody,
<br>> Does anybody why GROMOS96 lead to this error when I try to run cnvtop,
<br>> where topology.g87 is a topology for GROMOS87 generated by PRODRG
<br>>
<br>> This is the script:
<br>> rm -f fort.*
<br>> #---input units
<br>> ln -s topology.g87
fort.40 # molecular topology
<br>>
<br>> #----output units
<br>> ln -s topology.g96
fort.20 # final coordinates
<br>>
<br>> #---run the program
<br>> /usr/local/gromos96/cnvtop.64
<br>>
<br>> and this is the result of cnvtop.64:
<br>>
<br>> Scotty's CNVTOP Program!
<br>> $Id: cnvtop.f,v 1.15 1996/10/10 16:43:15 wscott Exp $
<br>> CNVTOP expects a binary GROMOS87 topology file on
<br>> unit 40.
<br>> It writes a GROMOS96 topology file to unit 20.
<br>> ORDTOP: Error reading NRATT!
<br>>
<br>> Thanks in advance,
<br>> Cheers
<br>> Ruben
<br>>
<br>>
<br>> --
<br>> ___________________________________________
<br>>
<br>> Rubén Martínez-Buey. PhD student
<br>> Protein Function and Structure Dept. Lab. 352
<br>> Centro de Investigaciones Biológicas (CIB-CSIC)
<br>> C/ Velázquez, 144 28006 MADRID
<br>> Tlf: +34-91-561 18 00 ext. 4380
<br>> ___________________________________________
<br>>
<br>>
<br>>
<p>##############################################################################
<p>Dr. Daan van Aalten
Wellcome Trust CDA Fellow
<br>Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
<br>Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
<br>School of Life Sciences
E-mail: dava@davapc1.bioch.dundee.ac.uk
<br>Univ. of Dundee, Dundee DD1 5EH, UK WWW: <a href="http://davapc1.bioch.dundee.ac.uk">http://davapc1.bioch.dundee.ac.uk</a>
<p> O
C O
C Visit the PRODRG server
to take
<br> "
| "
| the stress out of your
topologies!
<br> N--c--C--N--C--C--N--C--C--N--C--C--O
<br> |
" |
" <a href="http://davapc1.bioch.dundee.ac.uk/">http://davapc1.bioch.dundee.ac.uk/</a>
<br> C-C-O
O C-C-C O
programs/prodrg/prodrg.html
<br> "
<br> O
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<pre>--
___________________________________________
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
___________________________________________</pre>
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