You can use editconf to directly convert a .pdb file into .gro format. -Justin
Quoting maria goranovic <[EMAIL PROTECTED]>: > 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 > ====================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://bevanlab.biochem.vt.edu/Pages/Personal/justin/ ====================== _______________________________________________ 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
