Re: amber-developers: About calculating the minimum imaged distance

From: Thomas Cheatham III <>
Date: Tue, 25 Sep 2007 17:10:49 -0600 (Mountain Daylight Time)

> The program ptraj may give out the incorrect minimum imaged distance
> between two atoms when the non-imaged distance between the atoms is

This is now fixed in the amber10 release; also, this new version of ptraj
"gracefully" handles PDB overflow now-- instead of dumping ****'s, if the
atom number exceeds the max allowed by the PDB format, the count starts
over; likewise, if the residue number exceeds 9999 it is started over but
also a new chain identifier is added (starting with A, then B, ...).

If people have better suggestions on how to handle this, let me know (this
is mostly for viewing PDB's with lot's of water or very large systems
as most viewing programs choke on the ****'s).

Also, there is still an issue if you try to image *after* rms fitting as
the box frame of reference is not rotated; if someone knows easily how to
handle this (i.e. rotate the box frame) that may be helpful.
Alternatively, I may try to keep the total/overall rotation matrix at each
step in the ptraj process, such that if a rotation was done, it is undone
prior to imaging, imaged and then re-rotated (messy, but it will work)...


\-/ 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
Received on Wed Sep 26 2007 - 06:07:27 PDT
Custom Search