If I am not wrong, what you want to do is to build a topological file correctly for a cyclic peptide. You can do this: For example, your peptide has 5 (n=5) aa: CAAAD, You can build easily a linear topology file for a six (n+1) aa peptide chain ( with -ter switch answered by none): CAAADC, the last one should be the same as the first one. Then you can change the atom number for the last AA to the number for the first aa by just substracting the total number for the 5 AA from the atom number larger than that.
Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, August 17, 2006 10:51 PM To: Discussion list for GROMACS users Subject: Re: Θέμα: Re: [gmx-users] cyclic peptides Efi Mantzourani wrote: > Hi David, > > had a look for the specbond entry, but apparently it is for creating a > bond between ligand and receptor. I don't have that. Mine is not a > special bond. it is just that pdb2gmx tries to find a terminus for all > the chains. just try it anyway. you may have to sepcify the specific residue type of the N-terminus and C-terminus. > > */David van der Spoel <[EMAIL PROTECTED]>/* έγραψε: > > Efi Mantzourani wrote: > > Hi all, > > > > I am trying to run a gromacs trajectory on a ligand-receptor > complex, > > where the ligand is a head-to-tail cyclic peptide. I add the -ter > option > > in the pdb2gmx command, so that i can turn off the charged > termini in > > the peptide. Unfortunately, it will only work keeping the N > terminus as > > -NH2 (meaning it will add two hydrogens on the resulting > structure) or > > as N (in this case it doesn't add any hydrogens). They are both > wrong, > > as I want one hydrogen, like in a normal peptide bond. If i try to > > change the resulting files manually its a pain! The gro file is easy > > enough, but the topology file has to be altered so that the added > > hydrogen is in the correct atom and residue serial number. That > means i > > have to change all the remaining atoms, all angles, dihedrals > etc. Its > > just impossible as my complex has about 3.000 atoms! Any > suggestions??? > > try making a specbond entry, you have to make sure that the coordinates > are OK. please report back if succesfull. > > > > > ------------------------------------------------------------------------ > > Χρησιμοποιείτε Yahoo! > > Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail > διαθέτει την > > καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων > > http://login.yahoo.com/config/mail?.intl=gr > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users@gromacs.org > 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 > > > ------------------------------------------------------------------------ > Χρησιμοποιείτε Yahoo! > Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την > καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων > http://login.yahoo.com/config/mail?.intl=gr > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users@gromacs.org 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
