AMBER Archive (2005)

Subject: AMBER: inconsistent ordering in an improper dihedral of TRP

From: Sanghyun Park (spark7_at_stanford.edu)
Date: Sun Feb 06 2005 - 22:38:03 CST

Hi,

The ordering of the improper dihedral CD1-CD2-CG-CB is inconsistent
when there are multiple TRP residues. Here is an example:

$ tleap
> source leaprc.ff99
> x = sequence { ACE TRP TRP NME }
> saveamberparm x prmtop inpcrd
> quit

$ rdparm prmtop
RDPARM MENU: dihedrals

...
B 196: 1.100 3.14 2.0 :2_at_CD1 :2_at_CD2 :2_at_CG :2_at_CB
(15,28,14,11)
...
B 198: 1.100 3.14 2.0 :3_at_CD2 :3_at_CB :3_at_CG :3_at_CD1
(52,35,38,39)

When there are more than two TRP residues, the first one follows the
order CD1-CD2-CG-CB and all the others CD2-CB-CG-CD1.

I am using Amber 8. Thanks.

spark

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