Re: [AMBER] LEaP Error/questions.

From: Sam Walsworth (Researcher) <"Sam>
Date: Wed, 13 Jan 2021 20:41:01 +0000


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.

Essentially, it seems that tLEaP recognises the atom names in the .lib file ('> loadamberparams frcmod.NADH' followed by '> loadoff NADH.lib') and the PDB file ('> complex = loadpdb 1i10_final.pdb') both match but then hasn't connected the heavy atoms-hydrogens as the NADH.lib file instructs. The other ligand I'm using (pyruvate, using NADH as a cofactor; PYR-NADH) has formed its bonds correctly according to tLEaP/cpptraj. 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.
From: David A Case <>
Sent: 13 January 2021 16:11
To: AMBER Mailing List <>
Subject: Re: [AMBER] LEaP Error/questions.

On Wed, Jan 13, 2021, Sam Walsworth (Researcher) wrote:

>With regards to ParmEd, similarly couldn't find anything on Jason Swails'
>github describing how to list present bonds.

Type "help" at the parmed prompt; you will see a command called
"printBonds". Then type "help printBonds" to get detailed information about
how to use this.

But cpptraj is much better if you don't know which bonds might be bad.

...hope this helps...dac

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