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
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 -- 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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
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