Re: [AMBER] LEaP Error/questions.

From: Sam Walsworth (Researcher) <"Sam>
Date: Fri, 15 Jan 2021 18:58:38 +0000

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

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From: David A Case <>
Sent: Thursday, January 14, 2021 10:15:21 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] LEaP Error/questions.

On Wed, Jan 13, 2021, Sam Walsworth (Researcher) wrote:
>Following cpptraj, I've found out that the erroneously long bonds
>in my NADH ligand are all due to heavy atoms bonding to the
>wrong hydrogens. Having read through NADH.lib (originally from
>$AMBERHOME/dat/contrib/NADH_and_NAD+/), I've double checked that my PDB
>atom names for unit 'NAD' match the atom names in NADH.lib (I manually
>edited PDB atom names to match before I ran tLEaP). I also checked the
>connectivity table in the NADH.lib and realised every single hydrogen-heavy
>atom bond is incorrect.

I don't see that problem. A simple way to check the connectivities in the
NADH.lib file is this: fire up xleap, and give it these commands:

   loadOff NADH.lib
   edit NAD

xleap will just show bonds that are in the .lib file. I didn't see any
problems in doing this, that is, no evidence that the connectivities in the
NADH.lib file are wrong.

>The only thing I
>can think of is that I've edited my PDB file to match NADH.lib incorrectly
>without realising since it's not a random bond or two incorrect, every one
>of them is systematically wrong.

It seems possible that this might be your error. You could just remove
all hydrogens from the PDB file, and let tleap build them back in. That
would remove any mis-naming problem.

...good luck...dac

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Received on Fri Jan 15 2021 - 11:00:02 PST
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