AMBER Archive (2002)

Subject: Re: watershell in ptraj

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Tue Sep 24 2002 - 14:28:09 CDT

> I have a question about the watershell command in ptraj. The manual
> says: "...this option will count the number of waters within a certain
> distance of the atoms in the mask in order to represent the first and
> second solvation shells..." Now my question is when is a "water"
> molecule counted as beeing in the cutoff region? Is the center of mass,
> the oxygen or something else taken.

This is a good question since I failed to properly document this. It
looks like what I do is mark the solvent as being in the shell if any
atom of the solvent is within the shell. There is no center of mass
option. However, there is a solvent atom selection, so with water if you
only wanted to know if the oxygen was within the shell, then you would
specify :WAT_at_O as the solventmask. This routine ASSUMES that you have
solvent in the prmtop or have specified which residues are solvent with
the solvent command in ptraj. Let me know if this does not properly
clarify the functionality.

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418