Parichita, My guess is you only thought to have 1-6 linkage, because the atoms seemed so nicely involved in the .pdb file. But you'll have to define a bond explicitly or it won't be there to break in the first place. I think you need to read up on topologies, force fields and general background about simulating molecular systems. Chapter 5 is a must. If you continue on this path, note that sugar dihedrals, especially the ones connecting the rings, are complex. Check out Roberto Lins' paper on the 45a3 force field.
Tsjerk On 9/17/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > parichita parichita wrote: > > Hi again..... > > Thank you for your help.... > > I found my MANA in the ffG53a5.rtp and i can prepare > > the .gro and .top file from pdb2gmx. > > Now , i am facing another problem after solvation of > > my solute when i run the minimization the 1-6 linkage > > was broken ...... > > please help me out ........ > > "linkage was broken" doesn't help us help you. Please describe in detail > what you observed and why you think it was wrong. > > Mark > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
