AMBER Archive (2006)

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

From: Rahaman, Asif (
Date: Thu Aug 31 2006 - 16:34:50 CDT

Dear Professor Cheatham,
Thank you very much for your kind reply. I have done what you have suggested ( now the box looks OK) but still the structure of the system from .rst file and end of trajectory generated by ptraj is not the same.
You are right that topology file should have all the information. Let me explain a bit about setting up my system to resolve your confusion. I have created a crystal and put water molecule on top of it. Then I have set up periodic boundary condition. As Professor Case suggested in one of the comments in mailing list that I needed to change only the .crd file with correct box information. So I DID NOT change the TOPOLOGY file. Thus ptraj did not find that information when I ran.
Anyway, now that I have followed your suggestion I see the system initially OK but the end structure is still very much different from the structure that I get from the restart file. I out put my trajectory at every 100 steps and ran for 500000 steps. I do not know why the end structure from ptraj is different from the structure obtained from the .rst file. The structure from the .rst file looks reasonable; but the one at the end of ptraj is wired. (it messes up - waters come in side the crystal where as the structure obtained from .rst file with IWRAP = 1 option water stays either on top or bottom of the crystal - which is reasonable - I think).
Please let me know if you need additional information.
Thank you very much again for your kind reply.
With best regards, Asif


From: on behalf of Thomas Cheatham
Sent: Thu 8/31/2006 3:49 PM
Subject: RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj

> 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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