AMBER Archive (2006)

Subject: RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj

From: Thomas Cheatham (
Date: Thu Aug 31 2006 - 15:49:42 CDT

> I used IWRAP = 1. When I look at the .rst file with VMD, then I see
> correct structure of the system. But When I used 'ptraj' to analyze the
> .crd file, then system looks wired. I think - I am doing something wrong
> when running 'ptraj'. Here is my (script) file. Could someone
> please help me find out what I am doing wrong? I have looked at the
> manual and tried many options without success.
> --------------------------------------
> trajin md.crd 1 500 1
> trajout traj.crd
> box 24.9 24.7 24.7 90.0 90.0 74.8 24.9 24.7 24.7 90.0 90.0 74.8
> image center triclinic
> ----------------------------

The format of the "box" command is wrong, it should be

  box x 24.9 y 24.7 z 24.7 alpha 90.0 beta 90.0 gamma 74.8

Therefore, as written above, the command would have been ignored (and
you should have seen some kind of warning messages in the output).

Although the restrt file has ALL the box information, the standard ASCII
formated trajectory file only reports X, Y and Z. Thus, to get ptraj to
work correctly, you want:

  box alpha 90.0 beta 90.0 gamma 74.8

This should have been properly set upon reading the prmtop file so I am
somewhat confused as to why it is coming out "cubic".

If you still seem to have problems, I'd be happy to investigate the
prmtop/trajectory to see what is going wrong.


\-/ 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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