Dear Sir, I tried fitting the proteins of the trajectory in pymol as mentioned in your (Dr. Tsjerk's) tutorial, but later I tried using the trjconv -fit rot+trans to fit the proteins in the trajectory as you had mentioned.
I do not observe this degree of movement in protein when I view the trajectory along any 1-5 eigen vectors. This trajectory along any of these eigen vector is very minute and cannot be compared to that obtained after superposing the structure in the trajectory. Why is it so? Please let me know if I am understanding the concept wrong. Thanking you With regards M. Kavyashree On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M <[email protected]> wrote: > Thank you Sir! > > With regards > M. Kavyashree > > > On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar <[email protected]>wrote: > >> trjconv -fit rot+trans >> >> Cheers, >> >> Tsjerk >> >> On Jun 23, 2011 8:12 AM, "Kavyashree M" <[email protected]> wrote: >> >> Dear Users, >> >> Are there any tool for superposing the trajectory >> structures form MD. Please correct me if I am asking >> any illogical question. >> My previous question was regarding the trjconv output >> pdb trajectory, is there a way to superpose all these >> structures? >> >> Thank you >> With regards >> M. Kavyashree >> >> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M <[email protected]> wrote: >> > > Dear users, > > I... >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
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