Thanx Jagan. I just wanted to know the following:
Suppose we have a protein b.pdb in which I have done simulation getting the
files b.prmtop (topology file), b.mdcrd (coordinates of the trajectory). So
we find RMSD with respect to the reference structure b.inpcrd (initial
coordinates of b.pdb) as follows
$ ptraj b.prmtop <<x
> trajin b.mdcrd
> reference b.inpcrd
> rms reference out rms .CA,C,N
>x
Now if I want to compare the trajectory of b.pdb with another protein a.pdb
should I just replace b.inpcrd with a.inpcrd or do something else.
On Fri, Mar 19, 2010 at 3:26 AM, Jagan Mohan <o.jagan.gmail.com> wrote:
> Hey nicholus,
>
> You can do that using the RMSD Trajectory Tool in VMD 1.8.7. I hope that
> answered ur question. You can also do the same thing in ptraj.
>
>
> Best
> JM
>
> On Fri, Mar 19, 2010 at 12:40 PM, nicholus bhattacharjee <
> nicholusbhattacharjee.gmail.com> wrote:
>
> > Dear community,
> > We know that rms command in ptraj can be used
> to
> > calculated the RMSD of different snapshot with respect to some given
> > structure. Agani some visual sofwares like pymol can be used to calculate
> > RMSD between two different protein structures a.pdb and b.pdb. Now my
> query
> > is that is there a way to find the RMSD of different snapshot of b.pdb
> > simulation structure from a.pdb i.e at various time step I want to
> > calculate
> > the deviation of structure of b.pdb from a.pdb. Thanx in advance for
> > answering.
> >
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -{[O]}-
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 19 2010 - 01:30:03 PDT
