Re: Re: AMBER:

From: Qingning Shu <>
Date: Tue, 29 Aug 2006 12:26:34 -0400

Dear Sir
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.


-----Original Message-----
From: "David A. Case" <>
Date: Tue, 29 Aug 2006 08:09:23 -0700
Subject: Re: AMBER:

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

> I have a guanosine-analogue nucleotide ligand in protein complex. I obtained
> its prepin file accoding to the standard RNA residue. I set the atom types
> of C1', N9, C8, H8 as CT, N*, CK and H5 respectively. The dihedral angle
> C1'-N9-C8-H8 should be 0 degree. But during the MD process, this angle
> changed. It was not 0 degree anymore. I also tried relaxing the standard
> residue RG using xleap. This dihedral angle also changed. But since purine
> ring is conjugated, this angle should maintain at 0 degeee. Is it the
> problem of atom type?

The simple force field used in xleap is not the same one used in sander, and
it might miss a double-bond assignment. So you might try minimizing RG in
sander to see what happens. If that works OK, you could look for differences
between it and what you have.

You can use the "dihedrals" command of rdparm to print out what dihedral
angle terms there are in the force field.

You didn't say what your residue looked like after minimization. Is the
problem with the H8 atom or the C1' atom (or both)? Is the 5-membered ring
distorted as a whole, or are just some atoms misplaced? And how big is the
non-zero dihedral?


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Received on Wed Aug 30 2006 - 06:07:16 PDT
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