Re: [AMBER] Preparation of force field of zwitterion glycine molecule

From: David A Case <>
Date: Mon, 12 Nov 2018 08:36:44 -0500

On Sun, Nov 11, 2018, euq1702 wrote:
>I was wondering if someone could help me about the procedure of creating
>forcefield of glycine zwitterion for my case.

>But I am not sure whether the following procedure is correct or
>not. Because I at least found that O-C-O angle is not equivalated to
>130.25 (degree) even if it is in the diluted situation of glycine water

Two starting points: use parmed to see what the parameters are for your
CO2 group, with the printAngles command. You should see that the types
are c and o, and the equilibrium angle should be 130.25. If that is not
the case, something went wrong with the antechamber build.

You don't say what (average or minimized) angle you actually got. Since
atoms are subject to many forces, the average angle may deviate from the
target (130.25) for just the angle term itself. Relatively small
deviations are probably to be expected (although I have never studied
this particular functional group's geometry).

Finally, we don't know exactly how you created the prmtop file: it's
hard to understand what you mean by "replace directly from AM1-BCC to
CNDO". It would be more helpful if you show the exact commands that
were used to create your system.


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Received on Mon Nov 12 2018 - 06:00:07 PST
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