[gmx-users] getting a good .gro file from a pdb file while the topology is ready

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 8 09:09:56 CEST 2007


Adding a bit to Mark here...

> I am reasonably certain that if I put in more than
> > one copy of something which is in a .rtp file and _not_ in, say,
> ions.itp,
> > then it will be in both times in the .top file
> I think you are missing a point or two in comprehension here. The .rtp
> file is a database used only by pdb2gmx to help construct a
> correctly-connected topology for the residues in that database. I don't
> know about the behaviour of pdb2gmx on a structure file with multiple
> copies of the same molecule in different chains, but if it works, I
> expect it won't notice the same molecule is the product, and would thus
> produce two differently-named [ molecule ] sections for a dimeric
> system. In any case, the OP did not need to have been using pdb2gmx, and
> so the contents of the .rtp file are a red herring.

This is of course very common with multimeric proteins, and Mark is right:
pdb2gmx converts each chain it encounters to a "moleculetype". This has
nothing to do with whatever is in the .rtp database.

> (after all, two
> > different-position glycines are in twice in the .top file...).
> pdb2gmx has atoms and residues as its two levels of structure.

...and a third level: chains (which are translated to moleculetypes and are
a rough approximation of molecules).

The topology file has atoms and molecules as its two levels of structure. In
> the latter, residue names and numbers are retained purely for human
> convenience, say, in constructing index groups. Since these glycine
> residues are parts of molecules, they have to be replicated. This has
> nothing to do with replication of molecules, however. You could define
> multiple different [ molecule ] sections with different names for the
> same molecule and then have multiple entries in the [ molecules ]
> section, or you could have just one and have a single entry in the [
> molecules ] section. This brings us back to my original point that in
> the latter case the numbering of the atoms in [ molecule ] sections does
> not need to correspond to the structure file.
Someone should definitely (re)read Chapter 5 of the manual... (and it's not
Mark ;)).



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
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