> 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 - 09:30:04 PST
