Re: [AMBER] Ptraj: Hbond and Bfactor analyses

From: Thomas Cheatham <>
Date: Mon, 24 Jan 2011 16:04:14 -0700 (Mountain Standard Time)

> 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

> 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).


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Received on Mon Jan 24 2011 - 15:30:02 PST
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