Re: [AMBER] How to use GAFF2?

From: David A Case <>
Date: Thu, 3 Dec 2020 08:44:42 -0500

On Wed, Dec 02, 2020, Alexander Izvorski wrote:
>I'm trying to figure out how to use GAFF2 in antechamber/tleap.
>antechamber -i lig_in.mol2 -fi mol2 -o lig.mol2 -fo mol2 -c bcc -s 2 -rn LIG
>I noticed that "-at gaff2" is a possible option here - is it needed?


>what happens is a bunch of errors when running tleap later,
>"Error! Could not find bond parameter for: ns - ca" and similar

Can you provide a small example that shows this error?

>2. Run parmchk: "-s gaff2" enables GAFF2 here
>3. Run tleap: source leaprc.gaff2 loads GAFF2

Above are correct.

>This works using sustiva.mol2

Since it works for sustiva, we would need to see the case that fails. I
use gaff2 a lot, and have not seen the problem you describe.


cc-ing to junmei: can't we finally make gaff2 the default? I suspect
tons of people are still using gaff1 because one needs to make three
different changes.

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Received on Thu Dec 03 2020 - 06:00:02 PST
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