hi use #include "ffamber_tip3p.itp" instead #include "spc.itp" something like this check /usr/local/gromacs/share/gromacs/top/
Best regards, Andrey ---------------------------------------------------------------- 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: [EMAIL PROTECTED] Russia web: http://rnp-group.genebee.msu.su ----------------------------------------------------------------- ---------- Original Message ----------- From: Miguel Ortiz Lombardia <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tue, 28 Feb 2006 10:54:41 +0100 Subject: Re: [gmx-users] nucleic acis simulation > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > . > >> > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > - -- > 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: [EMAIL PROTECTED] > 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.1 (GNU/Linux) > > iD8DBQFEBB3hF6oOrDvhbQIRAkzKAKCc8Wok6hLm2M30J6O4T0/cBxamQgCfcbeh > S/WOOFec9Bjh55N2/tdKZtw= > =z9Xl > -----END PGP SIGNATURE----- > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ------- End of Original Message ------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
