Miguel Ortiz Lombardia wrote:
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Thank you Maik.
The AMBER ports are some I'm testing, sure.
BTW, I can't get it ready if I solvate the model. Everything goes fine
until grompp complains:
$> grompp -v -f em -c watered -o em -p nucT
(...)
- -------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108
Fatal error:
[ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
- -------------------------------------------------------
Any clues of what may be wrong?
order of bits in the topology file. chpater 5
If I don't solvate the model and remove the include line in the top file
for "sol.itp" the problem disappears...
Thank you,
Miguel
Maik Goette escribió el 28/02/06 09:54 :
Take the Amber-Port:
http://folding.stanford.edu/ffamber/
http://www.gromacs.org/topologies/uploaded_force_fields/ffamber_v1.0-doc.tar.gz
But beware of renaming atoms and residues before use. If you don't
pdb2gmx will inform you about problems.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Miguel Ortiz Lombardia wrote:
Dear all,
This is a question from someone just taking some timid steps in this
field. I'd like to know what force field, among those available in
Gromacs (v. 3.3) would you consider "better" for models containing
nucleic acids. As I understand this may be kind of a matter of taste and
could open a somehow sterile discussion, I would suggest you send your
opinion/arguments to my address. I would then compile a summary of the
answers and post it later.
Thanking you in advance for your kindness.
Cheers,
Miguel
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- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
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Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!
Georges Brassens
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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