Hi, if I understand well your question, you are dealing with SS bond, are you? in vmd you may not see the bond since vmd is guessing the SS bond based on the distance and not on your topology (actually the new version 1.8.5 should work better). What I think it should be important for your simulation is to check whether the SS bond is present in your topology in order to be used as it is during the gromacs simulation. Check for the specbond.dat file
I hope that it helps Regards andrea özge kül wrote: > After making Md simulation and getting the rmsd,gyration.. analyzing > graphics I looked at the VMD.Then I saw that the 2 chains are getting > splitting at a time.And then got together.So I could understand why the > graphics are so bad.Then I read the manual.It says I should use -merge > in pdb2gmx line if you have disulphite bridges.My molecule has 2 chains > that has disulfite bonds..Anything else that you know about this except > -merge? > > Thank you > özge > > Don't pick lemons. > See all the new 2007 cars > <http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE0OGRsc3F2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3Y2Fycw--> > at Yahoo! Autos. > <http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE0OGRsc3F2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3Y2Fycw--> > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org _______________________________________________ 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
