[gmx-users] nucleic acis simulation

[David van der Spoel]

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: 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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