[gmx-users] nucleic acis simulation

[Miguel Ortiz Lombardia]

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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?

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: molatwork at yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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