Re: AMBER: rdparm

From: Thomas Cheatham <>
Date: Sat, 16 Dec 2006 20:43:55 -0700 (Mountain Standard Time)

> I have to strip out all the water hydrogens from my simulation. I did it
> for the trajectory file but I don't understand the way to delete these
> atoms in the topology file.
> I tryied using the rdparm command, but I have just found a way to strip
> the water molecules (using the stripwater option).

There is no easy way to do this with ptraj/rdparm or any other program
within AMBER as "removing" atoms changes the topology and therefore the
parameters. "stripwater" in rdparm works because the only change is the
number of solvent residues, not the parameters (i.e. very little changes
in the prmtop file).

Potential solutions:

(1) MODERATELY DIFFICULT: modify ptraj/rdparm to allow deletion of atoms.
This would require removing the atom from many places, including any
charge/mass, bond, angle or dihedral it is involved in and also
repackaging of the nonbonded arrays (exclusion lists). This would also
require checking for complete removal of a given residue. The prmtop
writing routines would also need to be updated.

(2) LESS DIFFICULT, BUT TRICKY: create new library files for all residues
in your system without hydrogens and create new parameters as needed for
the missing values found when trying to build from this new library.

(3) POSSIBLY EASY: Make the hydrogens invisible; i.e. create library files
that zero the charge on hydrogens and zero all the dihedral terms
involving hydrogen. Turn on SHAKE for all hydrogens. (Then use the
original trajectories prior to stripping hydrogens).

Unless I am missing something, either (1) or (2) will require serious work
and I do not see what benefit will be gained... I would recommend keeping
the hydrogens or potentially converting to one of the united atom force
fields (where some of the hydrogens are removed).


\-/ 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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 17 2006 - 06:07:37 PST
Custom Search