Re: [gmx-users] g_rms -bm
Dear Justin Thank you very muchh Sogol From: Justin A. Lemkul jalem...@vt.edu To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, May 24, 2012 9:59 AM Subject: Re: [gmx-users] g_rms -bm On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote: Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have In this context, a bond means an actual chemical bond. A hydrogen bond is a nonbonded interaction. made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: /g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/ Does it show me how the ligand affects the active site residues bond angles? Potentially. And one more question, how can I study the ligand orientation in the active site? That depends on how you define orientation - internal metrics like dihedrals or angles between planes of groups in the ligand, relative measurements like its position with respect to protein residues, etc. All analysis tools are listed in the manual, Chapter 8 and Appendix D. It's quite a lot to read, but you'll be able to identify all the various things you can analyze and how the information might be connected across different analysis routines. -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] g_rms -bm
Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx Does it show me how the ligand affects the active site residues bond angles? And one more question, how can I study the ligand orientation in the active site? Sogol-- 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] g_rms -bm
Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx Does it show me how the ligand affects the active site residues bond angles? And one more question, how can I study the ligand orientation in the active site? Sogol-- 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] g_rms -bm
On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote: Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have In this context, a bond means an actual chemical bond. A hydrogen bond is a nonbonded interaction. made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: /g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/ Does it show me how the ligand affects the active site residues bond angles? Potentially. And one more question, how can I study the ligand orientation in the active site? That depends on how you define orientation - internal metrics like dihedrals or angles between planes of groups in the ligand, relative measurements like its position with respect to protein residues, etc. All analysis tools are listed in the manual, Chapter 8 and Appendix D. It's quite a lot to read, but you'll be able to identify all the various things you can analyze and how the information might be connected across different analysis routines. -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
