-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thank you Tsjerk.
Indeed, you're right. I'm using ffamber99, where the terminal residues have names starting with N or C, for N- and C-terminal. After reading your e-mail I re-run make_ndx and noticed that these terminal residues are not considered Protein, making grompp complain for the reason you exposed. Also, thank you for your advice on the bath. I'll follow it, of course. Cheers, Miguel Tsjerk Wassenaar wrote: > Hi Miguel, > > and then tried to make the index file again from the latter file. It > didn't work either. But I thought the problem might be in the 'pdb' > structure file produced by mdrun. > > Could this happen? > > > No. > > Is it possible that the three groups you give don't cover all the atoms > in your system? Besides, don't couple a handful of sodium atoms to a > private heat bath. Check the mailing lists... This has passed so many > times. In your case, go for two groups: Protein and Non-Protein, for > which you don't need an index file in the first place. > > Cheers, > > > Miguel > > > Cheers, > > Tsjerk > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > 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 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 v1.4.1 (GNU/Linux) iD8DBQFEDZd5F6oOrDvhbQIRAlhQAJsFBppMqrwVY0T+9PGeBsX0NQXQMQCfQw7f 3C2IBH4jgm+/6sOQQsYZJV8= =gQOd -----END PGP SIGNATURE----- _______________________________________________ gmx-users mailing list [email protected] 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
