AMBER Archive (2009)

Subject: [AMBER] leap and chirality

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Mon Mar 23 2009 - 04:54:29 CDT

Hello,

I am having some trouble with the chirality of a nonstandard reside
that I made. This residue has a head atom that is chiral, and I have two prep
files that reflect the two different chiralities. The res_a.prep file creates
a residue called AAA, while res_b.prep creates a residue called BBB, both are
mirror images of each other.

I load each into leap, and then combine them using the sequence
command. Using the command "x = sequence { AAA AAA }" and then viewing it in
xleap shows that the first AAA residue retains the correct chirality, while
the second AAA residue has the chirality flipped. This also holds true
for "sequence { BBB AAA }. However, if you view each residue by itself in
xleap, their chiralities are correct ("edit AAA", "edit BBB").

This problem also persists if I create longer sequences. I have also
tried to do this with both Cartesian and Z-matrix prep files. I would
appreciate it if someone could double check me on this, and point out what I
am doing wrong here.

I have attached the two prep files and the leap.in file. (I have a
personally made force field, which is not included, so there will be
parameters errors listed if you check - but this doesn't contribute to the
chirality problem.) I am using Amber9.

Thanks in advance.

Cheers,
Karl 

-- 
------------------------------------ 
Karl N. Kirschner, Ph.D.
Fraunhofer-Institute for Algorithms
    and Scientific Computing - SCAI
Department of Simulation Engineering
Schloss Birlinghoven
53754 Sankt Augustin, Germany
Tel: +49 (0) 2241-14-2052
Fax: +49 (0) 2241-14-1328
------------------------------------

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