AMBER Archive (2004)

Subject: Re: AMBER: Imaging problem

From: Thomas E. Cheatham, III (
Date: Fri Jul 30 2004 - 15:41:45 CDT

> I have a homodimer protein (each dimer has 99 residues), which during my
> periodic box-simulations (explicit waters) separated. I then tried
> Imaging using the following command:
> trajin wt.restrt_2500
> trajout wt2500imaged pdb
> center :1-99 origin
> image :100-198 origin center

  image origin center

is what you want here, but this doesn't explain the problem.

> The dimers do reform, but the problem is that now there are hugh VDW
> contacts between atoms. For example, I have an Oxygen from one monomer
> that is 1.97A to a Nitrogen of the other monomer.

My guess is that the box information is not being read properly from the
restart file and that the prmtop box information is overridding it.

Look at the last lines of the restart file where the box information is
kept and explicity set this in the ptraj script, before the center/image
commands, like below (exchanging the correct sizes).

box x 45.900 y 35.00 z 50.00

See if this works; in the meantime, I'll check to see if the box
information is not being properly pulled out of the restart file.

(note that if you read the trajectory, this problem should not occur, at
least in my experience, and if it does, there is something funny going


\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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