Dear Dr. Cheatham,
Thank you so much for your advice. I have a few follow-up questions.
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?
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.
Thank you again, and have a great day,
Kamali
On Mon, Jan 24, 2011 at 6:04 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > I'm trying to do Bfactor analysis on my system. I've combined
> calculations
> > of ion density maps and B factor, since I noticed that you need to
> calculate
> > the rmsd and average structure for both. I didn't think this would be a
> > problem, but I could be wrong:
>
> I would do this in three separate ptraj runs, (1) generate the average
> structure, (2) grid, (3) bfactor.
>
> (1) create avg
>
> rms first mass out A1+C37_all.rmsfit time 1 :1-73*
> average avg_A1+C37.pdb pdb*
>
> (3) b-factor
>
> reference avg_A1+C37.pdb
> rms reference mass out A1+C37_all.avgfit :1-73
> atomicfluct out L3_Bfactor.dat :21-27 start 1 stop 200 offset 1 bfactor
>
> Note we normally do this by residue or by atom and you might as well do
> over all atoms or residues?
>
> > This is what my L3_Bfactor.dat file looks like:
> >
> > * 1 18.880716*
> >
> > I'm a little confused as to why I only get one value in my output file.
> I've
>
> The "bymask" averages the B-factor over all the atoms in the mask. You
> want "byatom" or "byres".
>
> > My next question has to do with the Hbonding facility in ptraj. One set
> of
> ...
>
> > HBOND SUMMARY:
> > Data was saved to series hbond_water_acceptor.dat,
> > data was sorted, intra-residue interactions are NOT included,
> > Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
> > Hydrogen bond information dumped for occupancies > 200.00
>
> Only those with occupancies > 200 are dropped.
>
>
> > And then my job appears to stop. There is never any
> hbond_water_acceptor.dat
> > written. Could this be because I haven't specified enough memory? I
> submit
>
> You named the "series" hbond_water_acceptor.dat not the output file
>
> hbond series foo out hbond_water_acceptor.dat
>
>
> Use "print" to set the occupancy to dump (set to 0.0 for all).
>
>
> --tec3
>
>
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>
>
>
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Received on Wed Jan 26 2011 - 09:30:05 PST
