AMBER Archive (2006)

Subject: Re: AMBER: Question about renaming a residue

From: Thomas E. Cheatham, III (
Date: Fri Feb 17 2006 - 17:46:27 CST

> I've created two different residues in the past and they were both called UNK.
> I didn't think about it as they were not used at the same time. However, now
> I DO want to use them as part of the same simulation. How would I change the
> name of one of them in such a way that xLeap recognizes them as different.
> I've tried re-naming things in the past, but the original name seemed to stay
> as part of it. Was I incorrect? How would you suggest going about this?
> (Just re-creating one of the residues as something other than UNK isn't an
> easy option as they were difficult to set up in the past.)

This is doable simply by editing the appropriate file, depending on what
file type you used.

For prep files, all you change is the three letter residue name at the
start of every residue in that file... (i.e. UNK below)

   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000

For LEaP .lib files, there are more changes necessary...

At the top of the file, the array "index array str" lists all the residue
names. Change the particular "UNK" entry you are interested in, then
every !entry.UNK to your new name say "RES", i.e. !entry.RES


\-/ 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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