Re: [AMBER] Ligand-Resp-Gaussian

From: David Case <>
Date: Mon, 22 Jul 2019 20:33:51 +0000

On Mon, Jul 22, 2019, Prasanth G, Research Scholar wrote:
>As sqm was giving high penalty scores for one of the ligands, I had
>followed these steps to process the same through gaussian -

Note the sqm (itself) is just a quantum chemistry program: it is not
providing penalty scores. parmchk2 does this, and it is not expected,
or necessary, that all penalty scores be zero.

>$parmchk2 -i LIG.prepi -f prepi -o LIG.frcmod
>The output file (LIG.frcmod) still has the penalty scores -

This is often the case. In your case, it's certainly worth trying
gaff2, to see if it has better coverage of your ligand. Parameters with
a higher penaltiy score might be worth looking at more closely, but I'd
certainly recommend just continuing with the files you have. As with
any force field calculation, be on the lookout for things that might not
be what your want.


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Received on Mon Jul 22 2019 - 14:00:01 PDT
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