Sir, Thank you for the detailed insight. As you mentioned It does not give much information. But the matrix that it would generate would only show whether a specific salt bridge (SB) exited at a given time within the cut-off (0.4).
I got your explanation. Yes water mediated SBs are also interesting. If I had a given set of known SB then I would have definitely gone for g_dist. Thank you very much. Kavya On Tue, Apr 2, 2013 at 10:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M <hmkv...@gmail.com> wrote: > > > Sir, > > > > This g_hbond will generate a matrix similar to > > what g_saltbr would have given in terms of variation > > of distance between two charge groups. > > > > > I suppose, in that sense, the output can be useful. > > > > I want to find out the variation of all the salt bridges > > in the protein over the trajectory, if I have to use g_dist > > with an index of positive atoms and another of negative > > atoms, then it will calculate the distance between the > > centre of mass of these two groups.. according to manual. > > > > > Yes, but that's not what I suggested you do. You would need an index group > for each residue individually, not "all negative atoms" and "all positive > atoms." That would definitely be useless. If you consider each residue > individually, you can get a very detailed look at what's going on. What > you're doing now is saying "a salt bridge exists if N and O atoms are > within 0.4 nm." Is that an accurate descriptor? Upon what precedent have > you based that assessment? g_dist will also show you frames where those > atoms may not be within 0.4 nm, but what about the case of water-mediated > interactions; are those not interesting, as well? What I think you should > be doing is approaching the problem from multiple perspectives to get a > real look at what's going on. > > -Justin > > > > So How can I use g_dist for this kind of calculation. > > I am little confused. > > > > If I take a cut of of 0.4nm (as we mention in g_saltbr), will > > it be wrong if I have to calculate salt bridges between > > these two indices - > > > > group 1: ASP_GLU_&_OD1_OD2_OE1_OE2 > > group 2: ARG_LYS_&_NZ_NE_NH1_NH2 > > > > Thank you > > Kavya > > > > > > On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 4/2/13 11:58 AM, Kavyashree M wrote: > > > > > >> Sir, > > >> > > >> Thank you very much for your reply. I wanted to calculate > > >> Salt bridge in the whole protein so i am not mentioning the > > >> residues involved. The problem with g_saltbr was that if I > > >> have to calculate the accessibility of these atoms it will be > > >> a problem because it gives the charge groups but not exact > > >> atoms. > > >> > > >> This is the reason I thought of using g_hbond. But I wanted > > >> clarification from experts in using this method. > > >> > > >> So Is there any problem if I use g_hbond? > > >> > > >> > > > Does this really give you any useful information? You'll get an output > > > file with putative contacts derived from an arbitrary cutoff for any > > > possible positive-negative pair defined in the index group. I think > the > > > g_dist approach is far more useful and gives you exact insight into > > > specific pairs. It takes a bit more prep work, but looping the > > > calculations is trivial to do to make them efficient. > > > > > > -Justin > > > > > > > > > Thank you > > >> kavya > > >> > > >> > > >> > > >> On Tue, Apr 2, 2013 at 9:03 PM, bipin singh <bipinel...@gmail.com> > > wrote: > > >> > > >> You can use g_dist with specific atoms indices to calculate > distances, > > >>> if you already have the information about atoms involved in salt > > >>> bridge interactions. > > >>> > > >>> On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M <hmkv...@gmail.com> > > wrote: > > >>> > > >>>> Dear users, > > >>>> > > >>>> Kindly clarify my doubt regarding salt bridge calculation. > > >>>> > > >>>> Thank you > > >>>> Regards > > >>>> Kavya > > >>>> > > >>>> > > >>>> On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M <hmkv...@gmail.com> > > wrote: > > >>>> > > >>>> Dear users, > > >>>>> > > >>>>> For calculating salt bridge in proteins I > > >>>>> am using g_hbond instead of g_saltbr. > > >>>>> > > >>>>> In g_hbond I use contact and mention two > > >>>>> indices consisting of > > >>>>> group 1: ASP_GLU_&_OD1_OD2_OE1_OE2: > > >>>>> group 2: ARG_LYS_&_NZ_NE_NH1_NH2: > > >>>>> > > >>>>> I use the command: > > >>>>> g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm > > >>>>> matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 50000 > > >>>>> > > >>>>> Is this approach correct? > > >>>>> > > >>>>> Thank you > > >>>>> Kavya > > >>>>> > > >>>>> -- > > >>>> gmx-users mailing list gmx-users@gromacs.org > > >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > >>>> * Please search the archive at > > >>>> > > >>> http://www.gromacs.org/**Support/Mailing_Lists/Search< > > 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< > > http://www.gromacs.org/Support/Mailing_Lists> > > >>>> > > >>> > > >>> > > >>> > > >>> -- > > >>> ----------------------- > > >>> Thanks and Regards, > > >>> Bipin Singh > > >>> -- > > >>> gmx-users mailing list gmx-users@gromacs.org > > >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > >>> * Please search the archive at > > >>> http://www.gromacs.org/**Support/Mailing_Lists/Search< > > 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< > > http://www.gromacs.org/Support/Mailing_Lists> > > >>> > > >>> > > > -- > > > ==============================**========== > > > > > > 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< > > 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< > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > * Please search the archive at http://www.gromacs.org/** > > > Support/Mailing_Lists/Search< > > 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< > > 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 > > > > > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://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? 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