AMBER Archive (2006)

Subject: Re: AMBER: minimization with my own charges

From: Thomas Cheatham (
Date: Thu Aug 31 2006 - 23:07:40 CDT

> Only the modified histidine residues will have the new charges in your
> saved .lib file. In order to make all of the histidine residues in your
> >
> > However, I did my may, and there was no problem.
> >
> > After editing the charge of a histidine, I saved the .lib file.
> > When I load the .lib file, other histidines have the original charges.

Using TI to change charges is overkill, as is hand editing of residues in
LEaP. What I would do is:

(1) Look at what files are being loaded into LEaP when I create the
parameters/topology for the protein of interest.

If this is parm94/99 or a modification, this is the commands:

loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib

(2) Copy those files to my local directory. If they are in the local
directory, these have precedence for loading over the ones in the AMBER

(3) Edit those files and make copies of the histidine residue of interest,
then change the name on the second (new) instance to a name not in use for
residues, such as HI1 or HI2.

(4) Change the charges on the new copies to do the modification of

(5) Change the name of the HIS residues of interest in the PDB to the new

Things to watch out for; if you are doing terminal histidines, you will
want to make modifications to the all_aminoct94.lib (C-terminus) or
all_aminont94.lib (N-terminus) library files.

There are multiple types of histidine residues, specifically, HIP
(doubly protonated, +charge), HID (H on delta position) and HIE (H on
epsilon) so you may want to make sure you are assigning the type you want.
If you do not care, by default HIS maps to HIE (which may or may not be
what you want).

Back to the new residue names, maybe I would do HE1 (for epsilon,
modification 1) and HD1 (for delta modification) rather HI1 to avoid

Editing the files by hand (either to create new libraries with these
modifed residues with new unused names or to modify *copies* of the
canonical files) is much easier than changing charges in LEaP.

One could also consider editing the prmtop by hand, but this is even more


\-/ 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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