AMBER Archive (2006)

Subject: Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files]

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Thu May 04 2006 - 17:45:21 CDT

Thanks again for this advice. I've been testing adding a restraint
instead of a bond, which runs. However, I'm doing a simulation on a
crystal as a test of the force field I've been using for some time on
the same species in aqueous solution. I have used this force field for
quite some time with no problem, so I was quite surprised to see this
error. I'm not sure if adding a restraint gives me the information I'm
looking for, because I'm only doing this simulation as a check. Does
anyone have more information about this error?

With thanks,
Jennie Thomas

Bill Ross wrote:

>>1-4: angle 914 916 duplicates bond ('triangular' bond) or angle
>>('square' bond)
>>
>>
>
>This warning can be ignored, since you are building a triangle
>with your bonds on purpose.
>
>
>
>>But, I think I actually need to remove this angle in order to run the
>>simulation to avoid the following error upon trying to do an energy
>>minimization:
>>
>> EXTRA POINTS: nnb too small!
>> nnb,ntot = 3456 7776
>>
>>
>
>I think this has to do with charge-only points, and sounds like
>a bug. You may be able to avoid it by using a restraint instead
>of a bond to replace the angle potential. I don't think you can
>remove an angle from the calc altogether.
>
>Bill
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