Re: 回复: Re: 回复: Re: 回复: Re: 回复: Re: [gmx-users] about using

David Mobley dmobley at
Mon Feb 18 17:58:13 CET 2008

I think I can probably shed a little bit of light here, although Mark
is getting close in the last chapter of his e-mail.

Basically, pdb2gmx works well for parameterizing proteins, which the
chromophore in question isn't, I'm sure. Since we do lots of
protein-ligand simulations, where the ligand is not well-handled by
pdb2gmx, and since we like the GAFF (Amber) small molecule force
field, we have this script which works well for setting up
small molecules in AMBER and then converting them to get gromacs .top
and .gro files.

Xi, what you need to do is something like this:
1) Generate a .top and .gro of your protein only using pdb2gmx.
2) Generate a .top and .gro of your ligand (chromophore) using
3) Generate a combined .top and .gro by:
a) For the .top: Turning your ligand .top into a .itp file, as Mark
mentions, and including it in the protein topology file. You'll have
to see the manual to figure out differences between a .top and a .itp
b) For the .gro: There are several options here; you'll have to decide
between them by reading the manual or your own preferences. You can
either (i) manually (or using a script) generate one by combining the
ligand and protein .gro files; (ii) instead of a .gro, use a pdb file
(with all hydrogens, in the appropriate order) rather than a gro file
as input for grompp or the other gromacs tools. There may be other
ways as well.

Anyway, where you are at present is apparently step (3).

Hope that helps.


2008/2/17 Mark Abraham <Mark.Abraham at>:
> xi zhao wrote:
> > Dear sir:
> > Is my english weak?
> Not particularly, but it isn't helping you describe clearly :-)
> > I want to simulate pdb:1O5P (
> > <>), I use amber force field parms in the gromacs.
> > Under this condition, pdb2gmx can not produce chromophore top in the
> > pdb,
> Why not? You need to tell us why it doesn't work!
> > so I use antechamber and to produce chromophore gro and
> > top files accoding to ffamber website. I do not know how to produce gro
> > and top of entire system.
> Search the GROMACS wiki for "topology file" and read chapter 5 of the
> GROMACS manual to work out how to turn your chromophore .top into an
> .itp file suitable to include in a GROMACS .top file. Then use whatever
> technique works for you to do the same with your structure file *without
> the chromophore* (e.g. pdb2gmx, or via leap and Then
> #include your chromophore .itp in that .top file, and give your
> protein+chromophore structure file and that last .top file to grompp.
> You will need a detailed knowledge of chapter 5 of the manual, and
> there's useful information on the wiki too, so read them!
> Mark
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