DimitryASuplatov wrote: > Hello, > > I am sorry for this stupid question. > > Lets say I have an index file of all chain A atoms. I want to calculate > RMS of chain A _backbone_ only. > > I run g_rms. It asks two questions: > 1/ Select group for least squares fit > 2/ Select group for RMSD calculation > > To the best of my understanding, I should answer "BACKBONE" to the first > question and enter group number corresponding to chain A index file to > the second one.
In your case you need to make an index file with a group of the backbone of chain a, do something like make_ndx -f x.gro chain a "ChA" & Backbone q then run g_rms with -n And give the ChainA-backbone group twice to g_rms. Best, Jochen > > Is that correct? > Thank you. > SDA > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > . > -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
