On Thu, 2006-06-08 at 15:14 +0200, Alessandro Mattozzi wrote: > Is it necessary to specify the atomtype in the index file or is it read from > the .gro file or the .tpr? Because i guess some data are needed (vdW radius) > to insert spheres in the free volume. > Thanx >
Index files generally contain only atomic indexes and group names. As such, they only specify sets of atoms, and there is no way of specifying any additional information in the index file. See the manual for slightly more information. Atomtype, name and such stuff is as far as I know indeed read from the structure file (for example a tpr-file). The point of making an index file in this case is, I guess, that make_ndx creates a group consisting of the non-dummies. Erik Marklund Ph.D. Student ICM, Molecular biophysics Uppsala University Sweden > Alessandro Mattozzi > M.Phil., Ph.D. student > Dept. of Fibre and Polymer Technology > Royal Institute of Technology > Stockholm, Sweden > > > > -----Original Message----- > From: [EMAIL PROTECTED] on behalf of David van der Spoel > Sent: Wed 6/7/2006 5:14 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Free volume: Pass and Gromacs > > Alessandro Mattozzi wrote: > > Hi all > > I wonder if anybody has been using Pass to measure free volume: I got > > these errors: > > > > -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. > > Suggestion: Do I have to remove all the dummies? > Yes. > > make an index file, it will have a suitable group for it. > > > > > -Segmentation fault > > Suggestion: I use trjconv to get a pdb; is it possible that I am doing > > some mistake in the conversion? > > > > Thanx > > > > Alessandro Mattozzi > > M.Phil., Ph.D. student > > Dept. of Fibre and Polymer Technology > > Royal Institute of Technology > > Stockholm, Sweden > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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 _______________________________________________ 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
