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.CD1 :2.CD2 :2.CG :2.CB
(15,28,14,11)
....
B 198: 1.100 3.14 2.0 :3.CD2 :3.CB :3.CG :3.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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Received on Mon Feb 07 2005 - 04:53:01 PST
