Re: [gmx-users] RMSD Calculation

Hey :) You probably want to fit on the protein and calculate the RMSD on the ligand. You may need to specify these groups in an index file. Hope it helps, Tsjerk On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" wrote: Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small molecule co

Re: [gmx-users] RMSD Calculation

Nancy wrote: Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011

[gmx-users] RMSD Calculation

Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] rmsd calculation of helix only

ravi sharma wrote: Hello everyone is there any idea how can i calculate rmsd for a given helix or all helix in a protein from a trejectory??? Create an index group, specifying only the residues you care to analyze, and pass it to g_rms. -Justin -Ravi Ravi Datta Sharma Lecturer, Bi

[gmx-users] rmsd calculation of helix only

Hello everyone is there any idea how can i calculate rmsd for a given helix or all helix in a protein from a trejectory??? -Ravi Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut   Send fr