[AMBER] Ptraj: Hbond and Bfactor analyses

From: Kamali Sripathi <ksripath.umich.edu>
Date: Mon, 24 Jan 2011 17:26:18 -0500

Dear Amber users,

My system is an RNA system composed of 73 nucleotides. I have a few
questions about 2 utilities in ptraj:

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:

*# measure the RMSD of the RNA*
*rms first mass out A1+C37_all.rmsfit time 1 :1-73*
*# Calculate a grid of 150 X 150 X 150 ?~E with grid density of 0.5 ?~E in
each direction*
*grid hdrv.grd 150 0.5 150 0.5 150 0.5 :Na+*
# Calculate the B-factor for the L3 loop
atomicfluct out L3_Bfactor.dat :21-27 start 1 stop 200 offset 1 bymask
# Calculate an average pdb structure upon which to superimpose the grid
*average avg_A1+C37.pdb pdb*
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
tried the "atomicfluct" command both with and without the "start", "stop",
and "offset" options, and I keep getting the same result.

My next question has to do with the Hbonding facility in ptraj. One set of
hydrogen bonds that I'm trying to calculate consists of those between
hydrogen bonding donor groups of the residues and water hydrogens:

*donor RCP N4*
*donor RCP N4*
*donor RC3 O2'*
*donor RC3 N4*
*donor RC3 O2'*
*hbond series hbond_water_acceptor.dat time 1.0 print 200 distance 3.5
angle 120 solventneighbor 6 solventacceptor WAT O H1 solventacceptor WAT O

This is what I see from ptraj:

PTRAJ: Successfully read in 20004 sets and processed 20004 sets.
       Dumping accumulated results (if any)

      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

  Dumping schematic of time series after each h-bond, key follows:
   | . - o x * . |
      0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy

  atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
  angle lifetime maxocc
 ---------------- ---------------------------------

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
this script to multiple cores, specifying a total of 800 MB. There is
nothing written in the error file or the output file.

I would really appreciate any thoughts on this!

Thank you all,
Kamali Sripathi
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Received on Mon Jan 24 2011 - 14:30:04 PST
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