[gmx-users] Re: Salt bridge Calculations
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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Salt bridge Calculations
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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-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 -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Salt bridge Calculations
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? 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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-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 -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Re: Salt bridge Calculations
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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-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 -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-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) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Salt bridge Calculations
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 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. 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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Salt bridge Calculations
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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-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/Searchbefore 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 listgmx-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/Searchbefore 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
Re: [gmx-users] Re: Salt bridge Calculations
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 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-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/Searchbefore 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
