Re: [AMBER] LEaP Error/questions.

From: David A Case <>
Date: Fri, 15 Jan 2021 15:41:17 -0500

On Fri, Jan 15, 2021, Sam Walsworth (Researcher) wrote:

>I agree that the connections in NADH.lib look correct having tested
>them. I'm wondering if the hydrogens I'm adding (using MolProbity) are
>going to the wrong locations, hence the long bonds

Ah....molprobity will use the official naming scheme from the components.cif
library maintained by the wwPDB. Those standards did not exist two decades
ago, or whenever Ross made the library.

The *simplest* thing is just to not add hydrogens, either via molprobity or
by hand, and to remove any hydrogens that may be there already.

I don't know the "best" procedure for building a new NADH library: one would
want to take advantage of improvements in nucleic acid force fields, and
certainly to use standardized atom and residue nomenclature. You might
check out the libraries from Ulf Ryde at the contributed parameters


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Received on Fri Jan 15 2021 - 13:00:02 PST
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