Re: [gmx-users] Salt bridge observation
On 4/4/13 12:27 AM, Kavyashree M wrote: Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f traj.xtc -s md.tpr -b 4000 -e 4000 -t 0.4 -sep 2. Files that were generated were filtered and only those having sb between ASP, GLU and ARG LYS were retained. 3. Further, out of these sbs, those which had the following atoms CG ASP, CD GLU, NE ARG, NH1 ARG, NH2 ARG, NZ LYS were retained. Calculation using g_hbond - It was done using the index file mentioned in my previous post using g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000 So essentially the final results in both are composed of sbs formed between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr while charged atoms in case of g_hbond. The comparison showed that all sbs from g_hbond were present in the output from g_saltbr. But g_saltbr had some additional sbs off-course between the same charged groups. But only the distance was greater than 4 Ang for ex- distance between NH2 ARG and OD2 ASP is 4.32Ang Since it considers charged group CG of ASP instead of OD2 ASP distance between NH2 ARG and CG ASP is 5.54 Ang So g_saltbr is doing something weird, though I don't see how it is possible to be honest. It's up to you to filter the information by what you believe to be useful. An NH2-CG salt bridge likely doesn't make any sense at all, anyway. -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 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] Salt bridge observation
Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Thanks Regards Kavya On Thu, Apr 4, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 12:27 AM, Kavyashree M wrote: Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f traj.xtc -s md.tpr -b 4000 -e 4000 -t 0.4 -sep 2. Files that were generated were filtered and only those having sb between ASP, GLU and ARG LYS were retained. 3. Further, out of these sbs, those which had the following atoms CG ASP, CD GLU, NE ARG, NH1 ARG, NH2 ARG, NZ LYS were retained. Calculation using g_hbond - It was done using the index file mentioned in my previous post using g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000 So essentially the final results in both are composed of sbs formed between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr while charged atoms in case of g_hbond. The comparison showed that all sbs from g_hbond were present in the output from g_saltbr. But g_saltbr had some additional sbs off-course between the same charged groups. But only the distance was greater than 4 Ang for ex- distance between NH2 ARG and OD2 ASP is 4.32Ang Since it considers charged group CG of ASP instead of OD2 ASP distance between NH2 ARG and CG ASP is 5.54 Ang So g_saltbr is doing something weird, though I don't see how it is possible to be honest. It's up to you to filter the information by what you believe to be useful. An NH2-CG salt bridge likely doesn't make any sense at all, anyway. -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/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 (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] Salt bridge observation
On 4/4/13 4:34 AM, Kavyashree M wrote: Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Now I remember how g_saltbr naming works. It measured distances between charge groups, and the file names are based on the first atom in the charge group, so CG indicates the gamma-carboxylate group of ASP, which includes both OD1 and OD2. -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 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] Salt bridge observation
Ok. Still the distance is beyond the mentioned cut-off. The distance of both OD1 and OD2 of ASP is more than 4 Ang from NH2 of Arg. Thank you Regards Kavya On Thu, Apr 4, 2013 at 2:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 4:34 AM, Kavyashree M wrote: Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Now I remember how g_saltbr naming works. It measured distances between charge groups, and the file names are based on the first atom in the charge group, so CG indicates the gamma-carboxylate group of ASP, which includes both OD1 and OD2. -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/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 (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] Salt bridge observation
On 4/4/13 5:18 AM, Kavyashree M wrote: Ok. Still the distance is beyond the mentioned cut-off. The distance of both OD1 and OD2 of ASP is more than 4 Ang from NH2 of Arg. The cutoff is applied per group, not per atom within the group, IIRC. So if the charge group at any time comes closer than 0.4 nm, you get an output file for it. -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 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] Salt bridge observation
On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Please provide a concrete example. Note that running g_saltbr and g_hbond (with the index files mentioned before) should not be expected to produce equivalent result. g_saltbr is relatively stupid; it considers any group with a charge ± 0.2 to be capable of participating in a salt bridge. In some cases, this will include methylene groups or others than are near the actual charged groups. Such behavior could easily account for whatever observation you're making. -Justin -- 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 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] Salt bridge observation
Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f traj.xtc -s md.tpr -b 4000 -e 4000 -t 0.4 -sep 2. Files that were generated were filtered and only those having sb between ASP, GLU and ARG LYS were retained. 3. Further, out of these sbs, those which had the following atoms CG ASP, CD GLU, NE ARG, NH1 ARG, NH2 ARG, NZ LYS were retained. Calculation using g_hbond - It was done using the index file mentioned in my previous post using g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000 So essentially the final results in both are composed of sbs formed between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr while charged atoms in case of g_hbond. The comparison showed that all sbs from g_hbond were present in the output from g_saltbr. But g_saltbr had some additional sbs off-course between the same charged groups. But only the distance was greater than 4 Ang for ex- distance between NH2 ARG and OD2 ASP is 4.32Ang Since it considers charged group CG of ASP instead of OD2 ASP distance between NH2 ARG and CG ASP is 5.54 Ang There are some 10 more such examples. I can send the calculations if requires. Thank you Regards Kavya On Wed, Apr 3, 2013 at 10:25 PM, Justin Lemkul jalem...@vt.edu wrote: On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Please provide a concrete example. Note that running g_saltbr and g_hbond (with the index files mentioned before) should not be expected to produce equivalent result. g_saltbr is relatively stupid; it considers any group with a charge ± 0.2 to be capable of participating in a salt bridge. In some cases, this will include methylene groups or others than are near the actual charged groups. Such behavior could easily account for whatever observation you're making. -Justin -- 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 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
