Search for John Kerrigan's enzyme-ligand tutorial. It explains in clear detail everything you will need to do. Ignore the part about using PRODRG for your chromophore, as you apparently already have this information from antechamber.
For the future, it would be more clear to post this type of information: 1. What structures (pdb/gro, doesn't really matter) you already have 2. What topologies you have, and how you generated them 3. Specific errors you are having (from pdb2gmx, etc), not simply "I cannot get top and gro for the whole complex." It leaves us wondering what you have or haven't tried doing. -Justin Quoting xi zhao <[EMAIL PROTECTED]>: > Dear sir: > Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber > force field parms in the gromacs. Under this condition, pdb2gmx can not > produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to > produce chromophore gro and top files accoding to ffamber website. I do not > know how to produce gro and top of entire system. > > Mark Abraham <[EMAIL PROTECTED]> дµÀ£º > xi zhao wrote: > > Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding > > gro top files, but I can only produce chromophore gro and top file using > > amb2gmx.pl .Are you clear ? > > No. If you have a structure file already, then you need to read what I > wrote earlier. If you don't have a structure file already, then you need > to read what I wrote earlier. If you have some problem getting an > existing AMBER structure+prmtop to convert properly, then you haven't > communicated that. If you haven't got an AMBER structure+prmtop, then > give up on amb2gmx.pl > > Try explaining your problem in English to a friend who doesn't fully > understand the science. Then apply the lessons you learned there to > describing the problem here :-) > > 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
