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Hi,
<br>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.
<br>Thanks a lot
<br>Cheers,
<p>Ruben
<br>
<p>Daan Virtual wrote:
<blockquote TYPE=CITE>Hi Ruben
<p>The problem here is that for historical reasons GROMOS87 is limited
to a
<br>maximum of 99 atoms, bonds, angles etc. This is simply because there
is
<br>only a two-character space for these parameters in the topology.
<br>Therefore, originally PRODRG could also only deal with < 100 atoms.
This
<br>limitation has now been removed but it does mean that the GROMOS87
output
<br>produced with > 100 atoms (or indeed > 100 bonds, angles etc.) contains
<br>rubbish (the ** in your file). This problem as such cannot be solved.
<p>However, I am quite willing to incorporate GROMOS96 format in PRODRG
<br>directly if somebody on this list con provide me with a full set of
<br>installation files and a manual.
<p>cheers
<p>Daan
<p>On Wed, 11 Sep 2002, Ruben Martinez Buey wrote:
<p>> Hi all,
<br>> I have a small molecule with more than 100 atoms/bonds/angles. When
<br>> PRODRG generates the GROMOS87 topology, an error occurs:
<br>> _____________________________
<br>> 29
<br>> DRG
<br>> 6672**3038 0 0 1 1 1 1
<br>> ______________________________________________________________________
<br>>
<br>> I want to use GROMOS96, so I would like to generate a molecular topology
<br>> for GROMOS87 with PRODRG
<br>> and convert to GROMOS96 with the program "cnvtop.64" included in
the
<br>> GROMOS96 software.
<br>> Can anyone help me?
<br>> Thanks a lot for your help
<br>> with best regards
<br>> Ruben
<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>>
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<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</blockquote>
<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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