<br>Hi,<br><br>Adding a bit to Mark here...<br><br><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> I am reasonably certain that if I put in more than
<br>> one copy of something which is in a .rtp file and _not_ in, say, ions.itp,<br>> then it will be in both times in the .top file<br><br>I think you are missing a point or two in comprehension here. The .rtp<br>file is a database used only by pdb2gmx to help construct a
<br>correctly-connected topology for the residues in that database. I don't<br>know about the behaviour of pdb2gmx on a structure file with multiple<br>copies of the same molecule in different chains, but if it works, I
<br>expect it won't notice the same molecule is the product, and would thus<br>produce two differently-named [ molecule ] sections for a dimeric<br>system. In any case, the OP did not need to have been using pdb2gmx, and
<br>so the contents of the .rtp file are a red herring.</blockquote><div><br>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.
<br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> (after all, two<br>> different-position glycines are in twice in the .top file...).
<br><br>pdb2gmx has atoms and residues as its two levels of structure.</blockquote><div><br>...and a third level: chains (which are translated to moleculetypes and are a rough approximation of molecules). <br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The topology file has atoms and molecules as its two levels of structure. In<br>the latter, residue names and numbers are retained purely for human<br>convenience, say, in constructing index groups. Since these glycine<br>
residues are parts of molecules, they have to be replicated. This has<br>nothing to do with replication of molecules, however. You could define<br>multiple different [ molecule ] sections with different names for the<br>same molecule and then have multiple entries in the [ molecules ]
<br>section, or you could have just one and have a single entry in the [<br>molecules ] section. This brings us back to my original point that in<br>the latter case the numbering of the atoms in [ molecule ] sections does
<br>not need to correspond to the structure file.<br><br></blockquote></div><br>Someone should definitely (re)read Chapter 5 of the manual... (and it's not Mark ;)).<br><br>Cheers,<br><br>Tsjerk<br><br>-- <br>Tsjerk A. Wassenaar,
Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623