[AMBER] Ptraj: Hbond and Bfactor analyses

From: Kamali Sripathi <ksripath.umich.edu>
Date: Sat, 22 Jan 2011 11:33:28 -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 an average pdb structure upon which to superimpose the grid*
*average avg_A1+C37.pdb pdb*
*# Calculate the B-factor for the L3 loop*
*atomicfluct out L3_Bfactor.dat :21-27 start 1 stop 200 offset 1 bymask

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 mask :RA.N3,N7,N1,N9,N6
donor mask :RU.O2,O4,N1,N3
donor mask :RG.O6,N3,N7,N9,N1,N2
donor mask :RC.N3,O2,N1,N4
hbond series hbond_water_acceptor.out time 1.0 print 200 distance 3.5 angle
120 solventneighbor 6 solventacceptor WAT O H1 solventacceptor WAT O H2

This is what I see from ptraj:

  HBOND saved to series hbond_water_acceptor.out, inter-solvent hbonds will
not be included,

      data will be sorted, intra-residue interactions will NOT be included,
      Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information will be dumped for occupancies > 200.00
      Estimated memory usage for this hbond call: 44.41 GB
      donors: 717 acceptors: 271 frames: 20004
      solvent donors: 0 acceptors 40946

I have two questions regarding this output:

   - Why is the estimated memory usage so large? When I use the same command
   and syntax to calculate interactions between residues as Hbond acceptors and
   water oxygens, the estimated memory usage is only about 371 MB
   - Is there anyway to reduce the estimated memory?

Thank you all, and have a great weekend!

Kamali Sripathi
Graduate Student, Medicinal Chemistry
Walter Laboratory
930 North University
Ann Arbor, MI, 48109
AMBER mailing list
Received on Sat Jan 22 2011 - 09:00:04 PST
Custom Search