[gmx-users] g_helixorient help
Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_helixorient help
Hi All, Any suggestions? Thanks. On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan wrote: > Hi All, > I am trying to calculate the angle between the axes of two alpha helices > (say A and B) in my simulation. I have separate index files for the > residues pertaining to each helix. > > I calculated the tilt.xvg for both A and B. The output is slightly > confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. > What do these correspond to? (Helix A has 34 residues). Similarly for > bending_A.xvg > > How do I go about this? Is this the right way to calculate the relative > helix axis angle? > > Thanks, > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_helixorient help
Inter helical angle using *g_bundle * # 1. Do in make_ndx: # make_ndxGenerate indexes describing extremities of # the two helices. Select the CA of residues belonging #the extremities of each helix. make_ndx -f NAME.gro -o NAME_CROSSANGLE.ndx # Define other groups you need # Define 4 groups corresponding to the ends of the two helices # ... # q # 2. Do in a text editor: # Merge the 4 index groups, corresponding to helices ends, in order to get # two index groups, each containing either the beginning of the two # helices or the ends of the two helices. See g_bundle's online help. # The number of residues selected for each helix has to be the same. # 3. Do in g_bundle: # g_bundleGet coordinate of vectors describing the helices echo 0 1 | g_bundle -f NAME.xtc -s NAME.tpr -n NAME_CROSSANGLE.ndx \ -dt XX -b -e -na 2 -oa NAME_CROSSANGLE.pdb\ >& g_bundle.CROSSANGLE.out # -na 2; there are two axes this time # -oa NAME_CROSSANGLE.pdb ; to get the coordinates of the axes and check the angles given by the software # rm, Remove some unuseful files genererated by g_bundle: rm bun_len.xvg bun_dist.xvg bun_z.xvg bun_tilt.vxg bun_tiltl.xvg bun_tiltr.xvg # The first time, it might be helpful to open NAME_CROSSANGLE.pdb in rasmol or # vmd to visualize the data you are handling and check wether you define your # index correctly... and also two understand the structures of the data you # are handling. # The next part is dirty and could be automated with a smart script: # 4. Do in g_ traj # g_traj transform the .pdb trajectory in a file format easier to handle, # i.e a .xvg file. echo 0 | g_traj -f NAME_CROSSANGLE.pdb -s NAME_CROSSANGLE.pdb \ -ox NAME_CROSSANGLE.xvg >& g_traj.CROSSANGLE.out #In the header of the .xvg file, you have this: # @ legend string 0 "atom 1 X" # @ legend string 1 "atom 1 Y" # @ legend string 2 "atom 1 Z" # @ legend string 3 "atom 2 X" # @ legend string 4 "atom 2 Y" # @ legend string 5 "atom 2 Z" # @ legend string 6 "atom 3 X" # @ legend string 7 "atom 3 Y" # @ legend string 8 "atom 3 Z" # @ legend string 9 "atom 4 X" # @ legend string 10 "atom 4 Y" # @ legend string 11 "atom 4 Z" # @ legend string 12 "atom 5 X" # @ legend string 13 "atom 5 Y" # @ legend string 14 "atom 5 Z" # @ legend string 15 "atom 6 X" # @ legend string 16 "atom 6 Y" # @ legend string 17 "atom 6 Z" # 01.35431.23062.11210.85610.8589... # 201.40021.06922.04280.89430.7557... # 401.3591.07932.13410.86860.7528... # ...... # 5. Do in Microsoft Excel or equivalent # Import the .xvg file. You'll get a 19-column file. The first column # correspond to the time. The next 9 columns are (x,y,z) coordinates of 3 # points belonging to the vector describing the first helix and the next 9 # are coordinate of 3 points belonging to the second helix. # When this point is reached, you can define the vectors describing the # helices (by substracting coordinate of atom 3 and 1 and atom 6 and 4), # normalize them (by dividing the vector by their norm) and calulate their # dot-product in excel. # The dot product of two normalized vectors is the cosine of their # cross-angle. Disclaimer: Copied from an old gromacs discussion. On Thu, Jan 30, 2014 at 2:06 PM, rajat desikan wrote: > Hi All, > Any suggestions? > > Thanks. > > > On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan >wrote: > > > Hi All, > > I am trying to calculate the angle between the axes of two alpha helices > > (say A and B) in my simulation. I have separate index files for the > > residues pertaining to each helix. > > > > I calculated the tilt.xvg for both A and B. The output is slightly > > confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. > > What do these correspond to? (Helix A has 34 residues). Similarly for > > bending_A.xvg > > > > How do I go about this? Is this the right way to calculate the relative > > helix axis angle? > > > > Thanks, > > > > -- > > Rajat Desikan (Ph.D Scholar) > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > Dept. of Chemical Engineering, > > Indian Institute of Science, Bangalore > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Thanks and Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http
Re: [gmx-users] g_helixorient help
Thanks for the super detailed reply, Bipin. I will try this out! On Fri, Jan 31, 2014 at 3:04 PM, bipin singh wrote: > Inter helical angle using *g_bundle * > # 1. Do in make_ndx: > # make_ndxGenerate indexes describing extremities of > # the two helices. Select the CA of residues belonging > #the extremities of each helix. > make_ndx -f NAME.gro -o NAME_CROSSANGLE.ndx > # Define other groups you need > # Define 4 groups corresponding to the ends of the two helices > # ... > # q > > # 2. Do in a text editor: > # Merge the 4 index groups, corresponding to helices ends, in order to get > # two index groups, each containing either the beginning of the two > # helices or the ends of the two helices. See g_bundle's online help. > # The number of residues selected for each helix has to be the same. > > # 3. Do in g_bundle: > # g_bundleGet coordinate of vectors describing the helices > echo 0 1 | g_bundle -f NAME.xtc -s NAME.tpr -n NAME_CROSSANGLE.ndx \ > -dt XX -b -e -na 2 -oa NAME_CROSSANGLE.pdb\ > >& g_bundle.CROSSANGLE.out > # -na 2; there are two axes this time > # -oa NAME_CROSSANGLE.pdb ; to get the coordinates of the axes and > check the angles given by the software > > # rm, Remove some unuseful files genererated by g_bundle: > rm bun_len.xvg bun_dist.xvg bun_z.xvg bun_tilt.vxg bun_tiltl.xvg > bun_tiltr.xvg > > # The first time, it might be helpful to open NAME_CROSSANGLE.pdb in rasmol > or > # vmd to visualize the data you are handling and check wether you define > your > # index correctly... and also two understand the structures of the data you > # are handling. > > # The next part is dirty and could be automated with a smart script: > > # 4. Do in g_ traj > # g_traj transform the .pdb trajectory in a file format easier to handle, > # i.e a .xvg file. > echo 0 | g_traj -f NAME_CROSSANGLE.pdb -s NAME_CROSSANGLE.pdb \ > -ox NAME_CROSSANGLE.xvg >& g_traj.CROSSANGLE.out > #In the header of the .xvg file, you have this: > # @ legend string 0 "atom 1 X" > # @ legend string 1 "atom 1 Y" > # @ legend string 2 "atom 1 Z" > # @ legend string 3 "atom 2 X" > # @ legend string 4 "atom 2 Y" > # @ legend string 5 "atom 2 Z" > # @ legend string 6 "atom 3 X" > # @ legend string 7 "atom 3 Y" > # @ legend string 8 "atom 3 Z" > # @ legend string 9 "atom 4 X" > # @ legend string 10 "atom 4 Y" > # @ legend string 11 "atom 4 Z" > # @ legend string 12 "atom 5 X" > # @ legend string 13 "atom 5 Y" > # @ legend string 14 "atom 5 Z" > # @ legend string 15 "atom 6 X" > # @ legend string 16 "atom 6 Y" > # @ legend string 17 "atom 6 Z" > # 01.35431.23062.11210.85610.8589... > # 201.40021.06922.04280.89430.7557... > # 401.3591.07932.13410.86860.7528... > # ...... > > # 5. Do in Microsoft Excel or equivalent > # Import the .xvg file. You'll get a 19-column file. The first column > # correspond to the time. The next 9 columns are (x,y,z) coordinates of 3 > # points belonging to the vector describing the first helix and the next 9 > # are coordinate of 3 points belonging to the second helix. > > # When this point is reached, you can define the vectors describing the > # helices (by substracting coordinate of atom 3 and 1 and atom 6 and 4), > # normalize them (by dividing the vector by their norm) and calulate their > # dot-product in excel. > # The dot product of two normalized vectors is the cosine of their > # cross-angle. > > Disclaimer: Copied from an old gromacs discussion. > > > > On Thu, Jan 30, 2014 at 2:06 PM, rajat desikan >wrote: > > > Hi All, > > Any suggestions? > > > > Thanks. > > > > > > On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan > >wrote: > > > > > Hi All, > > > I am trying to calculate the angle between the axes of two alpha > helices > > > (say A and B) in my simulation. I have separate index files for the > > > residues pertaining to each helix. > > > > > > I calculated the tilt.xvg for both A and B. The output is slightly > > > confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. > > > What do these correspond to? (Helix A has 34 residues). Similarly for > > > bending_A.xvg > > > > > > How do I go about this? Is this the right way to calculate the relative > > > helix axis angle? > > > > > > Thanks, > > > > > > -- > > > Rajat Desikan (Ph.D Scholar) > > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > > Dept. of Chemical Engineering, > > > Indian Institute of Science, Bangalore > > > > > > > > > > > -- > > Rajat Desikan (Ph.D Scholar) > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > Dept. of Chemical Engineering, > > Indian Institute of Science, Bangalore > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > *
