Hi Niyaz, In pymol you can try this (assuming your proteins are called proteinA and proteinB):
import numpy d = numpy.array(cmd.get_model("proteinA").get_coord_list()) d -= numpy.array(cmd.get_model("proteinB").get_coord_list()) d = (d**2).sum(axis=1).tolist() tmp = list(d) alter proteinA, b=tmp.pop(0) alter proteinB, b=d.pop(0) spectrum b, rainbow, proteinA or proteinB Note this doesn't give the per-residue RMSD, but does the per-atom RMSD. The per-residue RMSD is a bit odd, as it doesn't tell you all about the backbone and doesn't tell you about the side chain. If you want the backbone-per-residue, choosing C-alphas should be good enough. For the side chains, you might want to consider dihedral angle RMSDs in stead. Hope it helps, Tsjerk On Mon, Oct 6, 2014 at 1:55 PM, niyaz.sabir <niyaz.sa...@gmail.com> wrote: > Dear Tsjerk, > > Thank you very much. You are always ready to help. > > I have understood and taken your note : "Whether it makes sense is another > question. The dynamics is usually coupled throughout the protein." > > With very best regards, > > Niyaz > > ----- Original Message ----- > *From:* Tsjerk Wassenaar <tsje...@gmail.com> > *To:* Discussion list for GROMACS users <gmx-us...@gromacs.org> ; > niyaz.sabir <niyaz.sa...@gmail.com> > *Sent:* Monday, October 06, 2014 1:13 AM > *Subject:* Re: [gmx-users] constraint and restraints > > Hi Niyaz, > > You can set position restraints for all atoms not in that residue range. > Whether it makes sense is another question. The dynamics is usually coupled > throughout the protein. > > Cheers, > > Tsjerk > > On Sun, Oct 5, 2014 at 10:03 PM, niyaz.sabir <niyaz.sa...@gmail.com> > wrote: > >> Dear GROMACS users, >> Is it possible with Gromacs and how could be done a simulation keeping >> almost all protein residues fixed except for instance resi 361-372 ? Will >> the extraction of resulting rmsd for each residue give some knowledge >> regarding its flexibility (mobility) ? >> Regards, N.S. >> -- >> 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. >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > -- Tsjerk A. Wassenaar, Ph.D. -- 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.