AMBER: [chirality.c] Atom did not match

From: Francesco Pietra <>
Date: Fri, 16 Nov 2007 09:09:10 -0800 (PST)

I am trying to use a POPC bilayer in Amber9. What I did:

(1) Created a 100x100A (smaller is not enough for my protein) POCP membrane.pdb
file with membrane plugin in VMD.

(2) Took a single POPC and successfully got prepin file with Antechamber/divcon
(which found no problems, as revealed by running parmchk).

(3) Using leaprc.ff99SB and gaff in xleap, loaded prepin. POPC seemingly OK
from "check POP" "edit POP".

(4) Command

model = loadpdb "membrane.pdb"


FATAL: In file [chirality.c], line 142
FATAL: message: Atom named C217 from POP did not match!
Hope not to have overlooked any precise answer from searching through the
mailing list archives. I do not understand the "chirality" because C217 is at
the penultimate methylene group of the longest fatty chain, so that no
chirality. Unless the wish of loading that way all the POPC molecules was
wrongly based .....

francesco pietra

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Received on Sun Nov 18 2007 - 06:07:49 PST
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