Hey nicholus,
All u have to do is change the reference according to what u want to do. If
you want to find rmsd of b's trajectory with respect to a then ur reference
pdb is a.pdb and vice versa.
Best
JM
On Fri, Mar 19, 2010 at 1:47 PM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> 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)
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> > >
> >
> >
> >
> > --
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>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Mar 19 2010 - 02:30:06 PDT
