Dear Dr. Simmerling,
I was hoping that you could make comments on if the following works for
the procedure that I described earlier:
trajin MDtraj1 1 1000 100 (one snapshot from each 100)
reference my_reference_snap (a reference snapshot)
trajout aligned_traj (includes 1000/100 = 10 snapshots)
rms my_reference_snap out rms .P (for an RNA molecule)
strip :WAT
strip :Cl-
strip :Na+
go
On Wed, 30 Mar 2005, Wen Li wrote:
> Dear Dr. Simmerling,
>
> Thanks for your help. What we want to do is using one snapshot (say a
> protein, not include ions and waters) of an MD trajectory as a reference
> aligns other snapshots to this reference, and then write out the
> coordinates of the aligned snapshots.
>
> I was hoping that you could provide information on which commands of
> ptraj should be used.
>
> Thanks,
> Wen
>
> On Tue, 29 Mar 2005, Carlos Simmerling wrote:
>
> > ptraj does this- if that's not what you want, you;ll have to be much
> > more specific.
> >
> > Wen Li wrote:
> >
> > >Hello everyone,
> > >
> > >I am wondering if there is a program available for a purpose of aligning
> > >snapshots along a trajectory to certain residues of a reference
> > >structure, and write out the coordinates of all aligned snapshots.
> > >
> > >Thanks,
> > >Wen
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Received on Wed Mar 30 2005 - 17:53:00 PST
