[gmx-users] nucleic acis simulation

[Andrey V. Golovin]

hi
use #include "ffamber_tip3p.itp" instead #include "spc.itp"
something like this
check /usr/local/gromacs/share/gromacs/top/

Best regards, Andrey
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Andrey V. Golovin
Ph.D, Assistant professor   tel: +7 (095) 939-5305  
Bioengineering and
Bioinformatics Department              
Moscow State University     fax: +7 (095) 939-3181
119899 Moscow               E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su
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---------- Original Message -----------
From: Miguel Ortiz Lombardia <molatwork at yahoo.es>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, 28 Feb 2006 10:54:41 +0100
Subject: Re: [gmx-users] nucleic acis simulation

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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 escribiС 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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> .
> >>
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> 
> - --
> Miguel Ortiz LombardМa
> Centro de Investigaciones OncolСgicas
> C/ Melchor FernАndez 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 libertИ
> Dans les jardins mal frИquentИs!
>                                                        Georges Brassens
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------- End of Original Message -------