AMBER: Re: FF problem: RG residue minimizes to non-planar structure

From: David A. Case <>
Date: Thu, 7 Sep 2006 11:53:33 -0700

On Tue, Aug 29, 2006, Qingning Shu wrote:

> Thank you for your reply. I did what you suggested and minimized the
> standard residue RG using sander (igb=1, Amber8). There is still a problem
> of yhe minimized RG. purine ring was fine but the C1' was off the plane. The
> dihedral angle of C1'-N9-C8-H8 was about 40 degree.

I cannot reproduce this problem, either in Amber8 or in later versions.
Which force field are you using?

Please do the following: run "rdparm prmtop", then issue the command
"dihedrals". This will print out a formatted form of the dihedrals. You
should see the improper about N9 about three lines from the bottom of this
output. For me, the end of the output looks like this:

     116: 0.000 0.00 2.0 :1.C4 :1.N9 :1.C1' :1.C2' (27,13,11,30)
     117: 1.175 0.00 2.0 :1.O2' :1.C2' :1.C3' :1.O3' (32,30,28,34)
E 118: 0.144 0.00 3.0 :1.O2' :1.C2' :1.C3' :1.O3' (32,30,28,34)
B 119: 1.000 3.14 2.0 :1.C4 :1.C8 :1.N9 :1.C1' (27,14,13,11)
B 120: 10.500 3.14 2.0 :1.C5 :1.N1 :1.C6 :1.O6 (17,20,18,19)
B 121: 1.100 3.14 2.0 :1.N2 :1.N1 :1.C2 :1.N3 (23,20,22,26)

Do you get something that looks any different?

You might have to post your prmtop file if nothing seems to come clear from


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Received on Sun Sep 10 2006 - 06:07:16 PDT
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