-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 David van der Spoel escribió el 28/02/06 11:25 : > Miguel Ortiz Lombardia wrote: > 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
The order of the elements in the topology file seem the same whether this is created using ffG43a1 or ffamber99. However, only the second prompts the error at the grompp step. I read the topology and molecule.itp file formats in chapter 5 of the manual (v. 3.2), but I was not able to spot the problem. Could you please be more precise? Thank you! Miguel - -- 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] 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.1 (GNU/Linux) iD8DBQFEBDkTF6oOrDvhbQIRArY5AJwN1OsHenfYKpaEK3OJbvYoxjkliwCfWc6u t+i++suqBCdxVWLLNRM28A0= =MVtb -----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
