Re: AMBER: Question bonds and angles in frcmod and lib files

From: Jennie Thomas <>
Date: Wed, 03 May 2006 08:54:43 -0700

Thanks very much for your idea. When I tried this, I cannot run a
minimization on the system because I get the following error:

 EXTRA POINTS: nnb too small!
 nnb,ntot = 3456 7776

I think this error may be because I have both bonds and angles defined
that are really redundant, even though the force constant for the bond
is set to zero. I posted a message regarding the "nnb too small"
message to the Amber mailing list earlier, but haven't found a solution
to this problem yet.

I'd be happy to send my .prmtop file, initial crd file, as well at the
.lib files and frcmod files I'm using if that would help.

Any ideas how fix this issue?

With thanks,

David A. Case wrote:

>On Wed, May 03, 2006, Jennie Thomas wrote:
>>I'm trying to more completely understand the information contained in
>>frcmod and lib files. I would like to change from using an angle to
>>constrain the geometry of my molecule to using an artificial bond with a
>>given force constant. I understand how to add a bond to both the lib
>>file and to the frcmod file. However, I don't understand how to delete
>>an angle from these files.
>Generally, you effectively delete the angle term by (re-)defining that angle
>potential with a force constant of zero.
>...hope this helps...dac
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Received on Thu May 04 2006 - 17:10:37 PDT
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