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