AMBER Archive (2003)

Subject: Re: AMBER: Any correct way to image a molecule ?

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Nov 13 2003 - 15:58:38 CST

> center origin
> image center familiar

I would use the commands below where :1-20 represents your DNA (assuming
you had 20 bases):

  center :1-20 mass origin
  image origin center

If it was in two strands, I would do:

  center :1-10 mass origin
  image origin center
  center :1-20 mass origin
  image origin center

I do not understand why the water and ions are not fully imaging or why
you have 4-8 boxes. On the other hand, I am also not exactly sure what
the "famililar" option will do for a rectangular box; the "familiar"
option is really intended for triclinic boxes (where the angles do not
equal 90.0 degrees).

> I'm now trying to find a way to do the same for the counter-ions and may
> be some water molecules. But there, i'm encountering an imaging problem
> : i've tried to be more precise in the centering, used masks, tried to
> not remove conter-ions or even water (that makes a big trajectory).

Obviously you have to keep the ions and water for the imaging part
(stripping or closestwaters can be done after the imaging).

> I've tried to change the size of the prmtop input file (the size of the
> box is somehow diminished during the run : coming from 62/52/51 to
> 60/50/50), but now i'm not able to image the counter-ions.

The box coordinates use read in from the trajectory unless you overwrite
them with the box command so I doubt this is the problem.

You could try updating to the new ptraj sources at

        http://www.chpc.utah.edu/~cheatham/software.html

If this still leads to problems, we can try to resolve them...

\ 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
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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