Thank you all for the replies and help. The main reason I was messing with pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro format file, which I could input into grompp. I understand grompp can take a pdb file for input as well. Does it not need any "box" information, like the box type, or the dimensions ? If it can infer these directly from the pdb, or these details can be specified in the .mdp file then my problems are solved.
I will look more carefully into the -h .. Thank you ! -Maria Message: 6 > Date: Thu, 04 Oct 2007 03:51:27 +1000 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file > while the topology is ready > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hydrogen takes up volume too... your equilibration will be less > troublesome if your whole system "fits" at the start of the equilibration. > > It sounds like it might be worth your while reading the introductory > part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea > what each tool is trying to do. Following a recipe without appreciating > what you're doing is fine, until you go to change the recipe, which is > what you're trying to do here. :-) > > Mark > > > ------------------------------ > > Message: 7 > Date: Thu, 04 Oct 2007 04:04:05 +1000 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file > while the topology is ready > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Allen Smith wrote: > > In message <[EMAIL PROTECTED]> > (on > > 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria > goranovic) > > wrote: > >> Hi, > >> > >> I had a large bilayer in .gro and .top gromacs format files > > > > Bilayer? I believe there are some specific things for doing planar > periodic > > boundary conditions (or planar infinite system conditions), but I am not > > familiar with them. > > Yeah but they're in the .mdp and not the issue here :-) > > >> which I truncated to make a smaller bilayer, and added some more water > >> molecules, using programs other than gromacs. The final output I have > is a > >> pdb file with complete solvation, and a topology file which I obtained > from > >> the original top file by simply changing the number of residues of each > >> group in the last section. > > > > Umm... the atom numbers (not just the numbers of residues) are going to > need > > to correspond between the .top and .gro files. > > I think the OP meant changing the number of molecules in the [molecules] > section of the .top file. I expect that within each molecule in the > structure file the order of the atoms must agree between with the > topology file. Certainly the order of the molecules in the [molecules] > section must correspond to that in the structure file. > > However, the atom numbers cannot (in general), match in order between > structure and topology file for any system with more than one copy of a > molecule (e.g. solvent). For simple solvated systems where one gets > focussed on the solute, it can look like correspondence is occurring and > thus might be necessary :-) > > Mark > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 42, Issue 11 > ***************************************** > -- Maria G. Technical University of Denmark Copenhagen
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