Quoting xi zhao <[EMAIL PROTECTED]>: > Dear sir : > Can you tell me a detail of procedure, I have only chromophore molecular > top,but I need entire top and gro for pdb + chromophore!
I would invest some serious time in background reading on conducting MD, especially with Gromacs, as there are plenty of resources available (check out wiki.gromacs.org, and read as much as you can!) Of special note, read here: http://wiki.gromacs.org/index.php/Beginners and http://research.ozreef.org/GROMACS_MD_Flowchart.pdf (linked from the above page, but worth highlighting) Try out lots of tutorials that do _not_ involve ligands/drugs to get a feel for the process of conducting some simple MD within Gromacs. Then search for John Kerrigan's tutorial for conducting a ligand-enzyme simulation. Protein structures can be obtained from the RCSB, but as for whether or not a crystal/NMR structure exists for your protein/chromophore of interest is anyone's guess. -Justin > > Mark Abraham <[EMAIL PROTECTED]> дµÀ£º > xi zhao wrote: > > Dear all users: > > I want to simulate a system ( protein + chromophore). I > > have had chromophore.gro and its top file using amb2gmx.pl,but I find I > > can not use them to translate PDB( protein + chromophore) file into gro > > and top files properly. So I need your advice about further procedure! > > Thank you very much > > You don't need a .gro file. See > http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file > The grompp utility will happily make a .tpr from your .mdp, your .top > file, and your well-formed .pdb file whose atom, residue and molecule > names and ordering matches the .top file. This last constraint also > applies to a .gro file! > > 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 > > > > --------------------------------- > ÑÅ»¢ÓÊÏä´«µÝÐÂÄê×£¸££¬¸öÐԺؿ¨ËÍÇ×Åó£¡ ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
