Re: [AMBER] leap mis-specified improper dihedral

From: Dean Cuebas <>
Date: Wed, 21 Dec 2011 00:34:23 -0600

Actually, I think I didn't explain my situation correctly.

According to the actual structure I should have a CT-CK-N*-CB improper
(the central sp2 is the N*),
Yet, xleap generates a .top file that contains CT-N*-CK-CB as the improper
(There is no improper in the actual structure that matches those atom
types with CK as the central atom in the improper, if
you apply the 3rd place rule).

Are CT-CK-N*-CB and CT-N*-CK-CB impropers describing the same thing?

rdparm shows: B 55: 1.000 3.14 2.0 :1.C1 :1.N9 :1.C8
:1.C4 (1,5,6,16)

Yet the the 3rd place rule says it should be (1,6,5,16)

Is this still not a problem? Just wanna be sure...

Thanks again, and sorry for my misleading initial question.


PS. Can someone remind me what the dihedral output in rdparm that start
with "E" means????

On 12/20/11 6:15 PM, "Bill Ross" <ross.cgl.ucsf.EDU> wrote:

>> > When I ran xleap, I obtain an improper that is (Y-X-Y-Y) where all the
>> > atoms are correct, except the sp2 center is in the second position of
>> > specified dihedral.
>> This is OK: a dihedral angle is unchanged when you reverse the order of
>> atoms.
>I remember deciding with Prof Kollman that the center atom should
>always be in the 3rd place. Since impropers should always be planar
>(since one can't depend on the sense of the cases with a duplicate
>atom type), perhaps it doesn't matter.
>AMBER mailing list

AMBER mailing list
Received on Wed Dec 21 2011 - 03:30:02 PST
Custom Search