Re: [AMBER] [Sender Not Verified] drug including B atom

From: David A Case via AMBER <>
Date: Thu, 16 Feb 2023 21:25:09 -0500

On Thu, Feb 16, 2023, laura zhang via AMBER wrote:

>above is the structure of the drug. I added hydrogen atoms in chimera. At
>the end of the step, chimera pointed out that the B atom needs assignment.
>I chose the geometry of B as tetragonal and with no subsitution. I am not
>sure if that is correct. Then when I added charge (neutralize it), it did
>not work. Maybe that is the reason why if failed? Could I know what kind
>of assignment on geometry and substitution I should use? Thanks a lot.

Hope this is not too much of a repeat: GAFF cannot handle boron. You might
see if a literature search leads to useful force field information. The
paramfit or mdgx programs can help with parameterization, but expect a fair
learning curve.

...good luck...dac

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Received on Thu Feb 16 2023 - 18:30:02 PST
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