Thanks a lot for all your help, Dr. Cheatham! Have a great week,
Kamali
On Wed, Jan 26, 2011 at 12:21 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > Regarding B-factor analysis, is there a way that I can monitor the
> changes
> > in the B-factor with respect to the starting coordinates? I think if I
> > reference the average pdb, I only get the average B-factors, is that
> right?
>
> Sure, just do the RMS to the first frame; however the definition of the
> B-factor is the average fluctuations about the average structure. If you
> do B-factor to the first structure, and during the MD you move away from
> this structure, then the B-factors will be larger.
>
> > Also, I think (based on what ptraj is telling me) that some of my Hbond
> > analyses quit before they are even read in. Ptraj gets here:
> >
> > File (../production190.traj.gz) is an AMBER trajectory (with box info)
> > with 100 sets
> > File (../production191.traj.gz) is an AMBER trajectory (with box info)
> > with 100 sets
> > File (../production192.traj.gz) is an AMBER trajectory (with box info)
> > with 100 sets
> > File (../production
> >
> > and then just stops. Is this because I haven't specified enough memory
> for
> > the job? No errors have occurred according to the error and log files.
>
> Probably; I do the h-bond in multiple separate runs with subsets of the
> donor/acceptor since otherwise the memory requirements are large since
> every possible donor-acceptor pair is "stored" and this grows rapidly.
>
> --tec3
>
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Received on Wed Jan 26 2011 - 16:30:04 PST
