Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis!
Francesco 2013/3/19 shahid nayeem <msnay...@gmail.com> > Thanks Francesco. > But my problem is exactly opposite. I do have a .top file containing > both chain linked by disulfide bridge. I ran the simulation. Now I > have extracted .xtc file for each chain separately and I want the > corresponding, separate .top file for each chain. when I separate the > pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is > absent in .xtc file. So the .top file generated this way has one atom > more as compared to .xtc file. > shahid > > On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri > <francesco.ot...@gmail.com> wrote: > > Hi, > > if you were able to obtain a simulation it means you had a valid .top > file! > > In any case, gromacs recognises disulfide basing on the distance beween > the > > SG atoms. > > In addition, the two chains are supposed to be in the same molecule. > > So, my advice is, remove all the TER from pdb (but the last one), leave > the > > chain id and use pdb2gmx > > with the option -chainsep ter. The result is supposed to be a topology > > where your chain are grouped in > > a single molecule,making possible to create the bridge, and at the same > > time you keep the chain name > > for future analysis. > > > > Francesco > > > > > > 2013/3/19 shahid nayeem <msnay...@gmail.com> > > > >> Hi > >> To be more clear I have .xtc file for a disulfide linked complex of > >> two chains. From this trajectory I can extract .xtc file for > >> individual chains. But when I generate .top file from individual chain > >> pdb I get one atom extra in .top file i.e. protonated SG of Cys which > >> I dont need in order to make my .xtc and .top file compatible. > >> Shahid > >> > >> On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> > > >> > > >> > On 3/18/13 12:35 PM, shahid nayeem wrote: > >> >> > >> >> Hi > >> >> Is it possible to write .top file from .xtc and .tpr using index.ndx > >> >> so that .top is available for tailormade components of simulated > >> >> protein. > >> >> > >> > > >> > All topology information is in the .tpr, but not in .top format. You > >> may be > >> > able to post-process the output of gmxdump to produce some hacked > >> version, > >> > but that's just a bit of a hand-waving guess. I don't really > understand > >> > what your objective is. > >> > > >> > -Justin > >> > > >> > -- > >> > ======================================== > >> > > >> > Justin A. Lemkul, Ph.D. > >> > Research Scientist > >> > Department of Biochemistry > >> > Virginia Tech > >> > Blacksburg, VA > >> > jalemkul[at]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/Support/Mailing_Lists/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/Support/Mailing_Lists > >> -- > >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists > >> > > > > > > > > -- > > Cordiali saluti, Dr.Oteri Francesco > > -- > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
