<div><BR>Dear sirs:</div> <div>Thank you for your advices!</div> <div>The problem has been wiped off !</div> <div><BR><B><I>David Mobley <dmobley@gmail.com></I></B> 写道：</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">I think I can probably shed a little bit of light here, although Mark<BR>is getting close in the last chapter of his e-mail.<BR><BR>Basically, pdb2gmx works well for parameterizing proteins, which the<BR>chromophore in question isn't, I'm sure. Since we do lots of<BR>protein-ligand simulations, where the ligand is not well-handled by<BR>pdb2gmx, and since we like the GAFF (Amber) small molecule force<BR>field, we have this amb2gmx.pl script which works well for setting up<BR>small molecules in AMBER and then converting them to get gromacs .top<BR>and .gro files.<BR><BR>Xi, what you need to do is something like this:<BR>1) Generate a .top and .gro of your protein only using pdb2gmx.<BR>2)
Generate a .top and .gro of your ligand (chromophore) using amb2gmx.pl<BR>3) Generate a combined .top and .gro by:<BR>a) For the .top: Turning your ligand .top into a .itp file, as Mark<BR>mentions, and including it in the protein topology file. You'll have<BR>to see the manual to figure out differences between a .top and a .itp<BR>b) For the .gro: There are several options here; you'll have to decide<BR>between them by reading the manual or your own preferences. You can<BR>either (i) manually (or using a script) generate one by combining the<BR>ligand and protein .gro files; (ii) instead of a .gro, use a pdb file<BR>(with all hydrogens, in the appropriate order) rather than a gro file<BR>as input for grompp or the other gromacs tools. There may be other<BR>ways as well.<BR><BR>Anyway, where you are at present is apparently step (3).<BR><BR>Hope that helps.<BR><BR>David<BR><BR><BR>2008/2/17 Mark Abraham <MARK.ABRAHAM@ANU.EDU.AU>:<BR>> xi zhao wrote:<BR>> > Dear
sir:<BR>> > Is my english weak?<BR>><BR>> Not particularly, but it isn't helping you describe clearly :-)<BR>><BR>> > I want to simulate pdb:1O5P (www.rcsb.org<BR>> > <HTTP: www.rcsb.org>), I use amber force field parms in the gromacs.<BR>> > Under this condition, pdb2gmx can not produce chromophore top in the<BR>> > pdb,<BR>><BR>> Why not? You need to tell us why it doesn't work!<BR>><BR>> > so I use antechamber and amb2gmx.pl to produce chromophore gro and<BR>> > top files accoding to ffamber website. I do not know how to produce gro<BR>> > and top of entire system.<BR>><BR>> Search the GROMACS wiki for "topology file" and read chapter 5 of the<BR>> GROMACS manual to work out how to turn your chromophore .top into an<BR>> .itp file suitable to include in a GROMACS .top file. Then use whatever<BR>> technique works for you to do the same with your structure file *without<BR>> the
chromophore* (e.g. pdb2gmx, or via leap and amb2gmx.pl). Then<BR>> #include your chromophore .itp in that .top file, and give your<BR>> protein+chromophore structure file and that last .top file to grompp.<BR>><BR>> You will need a detailed knowledge of chapter 5 of the manual, and<BR>> there's useful information on the wiki too, so read them!<BR>><BR>><BR>> Mark<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>><BR>_______________________________________________<BR>gmx-users mailing list
gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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