Capping peptides is non-trivial, so the error may have been introduced there - certainly the approach you stated is not what I or others have used successfully. There have been a number of posts discussing how to do this, check the archives.
----- Original Message ---- From: OZGE ENGIN <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, August 24, 2007 10:45:14 AM Subject: [gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem Hi gromacs-users, I want to simulate a box of that is composed of capped (ACE and NME to N and C termini, respectively) tryptophan molecules. As a first stage, I minimized single capped trp molecule, and then used it with genconf command along with the options -rot ans -nbox. In this case, I changed the gro file of capped trp molecule such that it was treated as a single molecule rather than three (cappes and the trp molecule itself). (It was necessary to be able to use that molecule with genconf command.) After that, I could obtain a box of trp molecules. However, when I looked at it by using VMD, I saw that some of them had unusual bonds. So it caused not to minimization of my system. The steepest descent minimization was terminated before the desired criterion was reached. Although I used a minimized capped trp molecule with genconf command, the resultant box contained some trp molecules that have unusual structures. How can I overcome that problem? Thanks in advance... Oz. _______________________________________________ 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 ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz _______________________________________________ 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
