The reason I commented about the use of your .tpr file is that, from your message, it seemed that you did not understand exactly how to use trjconv, and were perhaps using a different .tpr file (named topol.tpr) to simply satisfy trjconv. Your previous message said your grompp output produced a md.tpr file, which is what you should be using to conduct your analysis, and was what I was trying to clue you in on.
In order to get useful help, you must provide information that is self-consistent, otherwise we are to assume that you are shooting in the dark, so to speak. Also, take note of Tsjerk's message from earlier this morning; his advice about choosing the correct group for output is important. -Justin Quoting Anamika Awasthi <[EMAIL PROTECTED]>: > Justin I already tried this > > I tried this command---> > > trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole > > this was showing this error > > "can not open file > topol.tpr" > then > I repeated the same command with "-s topol.tpr" > > then > > trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump > > then > > g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr > > but now this is showing Fatal Error > > " Molecule in topology has atom numbers below and above natoms. you are > probably trying to use a trajectory which does not match the first 330 atoms > of the run input file. You can make a matching run input file with tpbconv." > > with regards > Anamika > > > > > > -- > Anamika Awasthi, PhD > DBT-Postdoctoral Fellow > Laboratory of Structural Biology > Centre for DNA Fingerprinting and Diagnostics (CDFD) > ECIL Road, Nacharam > Hyderabad 500 076 > INDIA > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
