Hi, 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 ;)). Cheers, Tsjerk -- 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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