Re: [gmx-users] Occupancy for a distance cut off
Thank you!! On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul wrote: > > > On 2/11/13 9:16 PM, ram bio wrote: >> >> Hi Justin, >> >> Thanks for the suggestion. >> >> I executed the following command: >> >> g_dist -f n101c2naclprod2-12nsvrpr.trr -s >> n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o >> N101Cbest2NACL606S336HG1.xvg >> >> and the output was distance calculated for every 10 frames in nm as under: >> >> t: 11870 336 SER 4166 HG1 0.239086 (nm) >> t: 11880 336 SER 4166 HG1 0.248868 (nm) >> t: 11890 336 SER 4166 HG1 0.231819 (nm) >> t: 11900 336 SER 4166 HG1 0.218495 (nm) >> t: 11910 336 SER 4166 HG1 0.233166 (nm) >> t: 11920 336 SER 4166 HG1 0.283512 (nm) >> t: 11930 336 SER 4166 HG1 0.239512 (nm) >> t: 11940 336 SER 4166 HG1 0.216938 (nm) >> t: 11950 336 SER 4166 HG1 0.220066 (nm) >> t: 11960 336 SER 4166 HG1 0.227595 (nm) >> t: 11970 336 SER 4166 HG1 0.247895 (nm) >> t: 11980 336 SER 4166 HG1 0.259074 (nm) >> t: 11990 336 SER 4166 HG1 0.228319 (nm) >> t: 12000 336 SER 4166 HG1 0.264722 (nm) >> >> So, my question is that now do maths and find percent frames that >> were above the 3.5 Å and expresses it relation to unity for occupancy. >> That is if i have 30 frames above 3.5Å out of 100, then the occupancy >> would be 0.7. >> >> Please advice if there is any other ways to do it.. >> > > Redirect the output into a file, count the number of lines in the file with > wc -l and you have the answer. > > > -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 -- 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] Occupancy for a distance cut off
On 2/11/13 9:16 PM, ram bio wrote: Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Redirect the output into a file, count the number of lines in the file with wc -l and you have the answer. -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] Occupancy for a distance cut off
Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Thanks, Pramod On Mon, Feb 11, 2013 at 7:19 PM, Justin Lemkul wrote: > > > On 2/11/13 6:15 PM, ram bio wrote: >> >> Dear Gromacs Users, >> >> I have a run a MD simulation on protein bound with ligand and ions >> using Gromacs 4.5.4. I am able to calculate the distances between ions >> and coordinating residues using g_dist. The output is in the form of >> xvg file, but I am looking for the occupancy for a cut off distance >> (3.5 Å) between ion and a particular residue atom during simulation. >> Please suggest. >> > > g_dist -dist 0.35 > > -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 -- 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] Occupancy for a distance cut off
On 2/11/13 6:15 PM, ram bio wrote: Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. g_dist -dist 0.35 -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
[gmx-users] Occupancy for a distance cut off
Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. Thanks, Pramod -- 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
