RE: AMBER: checkoverlap doubt [was: Post-MD minimization]

From: Thomas Cheatham <>
Date: Tue, 20 Jun 2006 16:28:36 -0600 (Mountain Standard Time)

> I have one more question. I would like to identify the structures from MD
> trajectory which have short contacts. For this purpose, when I use ptraj
> to check overlaps between atoms, (checkoverlap command of ptraj), how do I
> get the list of "flagged" atoms? In the output of my trajin script, it
> Dumping accumulated results (if any)"
> Where are these results dumped? How do I save them? (Unlike some other
> commands there is no "out" option for checkoverlap).

The checkoverlap command, as you note, does not dump output to a file. It
all comes to stdout. You can grep the output file for lines that start
with "OVERLAP: ". However, this may not be very useful as no frame number
is reported.

If no atoms overlap, nothing is output. You can change the cutoff for the
interaction (default is distance separation of less than 0.95 angstroms)
using the min keyword, i.e. the following will report on any atoms with
distances of less than 5.0 angstroms.

checkoverlap * min 5.0

This still may not be that useful. Better may be to use the hydrogen bond
utility to monitor distances (if you know the list of atoms you are
interested in), however this too only supplies summary information (not a
per frame data). This may show you interactions that you can then monitor
in the traditional way by measuring the distance directly.

Say you are interested in LYS NH3+ interactions with ASP CO2- and all N-H
or C=O backbone interactions...

donor ASP OD1
donor ASP OD2
acceptor LYS NZ HZ1
acceptor LYS NZ HZ2
acceptor LYS NZ HZ3
donor mask .O
acceptor mask :2-99999999.N :2-999999999.H

hbond series hbond out hbond_summary.dat time 1.0 angle -1.0 distance 3.5

...will monitor distances < 3.5A, no angle critera, and output the results
to hbond_summary.dat. This still does not dump the list of interactions
by frame but will show you schematically when/how much the interactions
are formed.

Good luck,

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Wed Jun 21 2006 - 06:07:15 PDT
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