[gmx-users] Hello

nikhil damle pdnikhil at yahoo.co.in
Tue Jul 14 08:30:52 CEST 2009

I am carrying out energy minimization of the protein peptide complex. But even after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide far away from the binding site. This did not happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar .mdp file is given for energy minimization. What could be possible reasons for such flying away of the peptide ? How should I fix the problem ?


Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090713/825d3de0/attachment.html>

More information about the gromacs.org_gmx-users mailing list