Quoting Jennifer Williams <jennifer.willi...@ed.ac.uk>: > > Hello > > I am studying a mesoporous silica for which there is no topology in > gromacs-to try to automate the process of generating a topology file > (x2top doesn?t work), I am using pdb2gmx (or rather trying to). > > I have parameters for my silica structure and have added a new section > for my molecule to the .rtp file, .atp file, atommass.dat, > atom_nom.dbl, nb.itp and bon.itp files. > > The problem is that when I use my .pdb file to generate a topology, > pdb2gmx checks for duplicates and removes almost all of my atoms. It > leaves only one of each type. I should have a few hundred of each atom > type?here is the output from pdb2gmx? > > Analyzing pdb file > There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms > chain #res #atoms > 1 ' ' 1 4284 > All occupancies are one > > All ok up to here?and then?. > > Processing chain 1 (4284 atoms, 1 residues) > There are 552 donors and 2580 acceptors > There are 1603 hydrogen bonds > Checking for duplicate atoms.... > Now there are 4 atoms. Deleted 4280 duplicates. > > Can anyone explain why this is happening? ?none of my atoms have the > same coordinates. Is there a file that I have forgotten to alter? Is > there is fix to turn off the checking of duplicate atoms? I don?t want > any of my atoms to be deleted!
You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. > > Below I paste an extract of my pdb file? > I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin > CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 > ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI > ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI > ??.. > ATOM 1153 O MCM 1 20.602 -18.404 -20.904 1.00 0.00 O > ATOM 1154 O MCM 1 20.602 -18.404 -1.945 1.00 0.00 O > ? > ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 > ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 > ..... > ATOM 3733 H MCM 1 -6.674 -18.381 -33.035 1.00 0.00 H > ATOM 3734 H MCM 1 -6.616 -18.600 -14.144 1.00 0.00 H > > Any advice appreciated, > > Thanks in advance > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php