If it works then you are right :)
2013/3/19 shahid nayeem <msnay...@gmail.com> > I did it. Simply I changed the name of Cys which forms interchain > dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 > forcefeild to run pdb2gmx. This gives a topology with same number of > atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 > forcefeild probably to form interchain disulfide bond reading from > specbond.dat. Am I right in generating such half disulfide bond > topology. > shahid > > On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri > <francesco.ot...@gmail.com> wrote: > > 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 > -- > 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