Re: [AMBER] LEaP Error/questions.

From: Sam Walsworth (Researcher) <"Sam>
Date: Mon, 11 Jan 2021 17:10:26 +0000

Hi David

I played around with the original PDB file and using pdb4amber and it mostly worked, except now I have HIE atoms not having a type (I believe I've seen issues regarding histidine protonation causing errors) and the NADH cofactor atoms types are not found. I'm using Ross Walker's contributed parameters for these ($AMBERHOME/dat/contrib/NADH_and_NAD+/NADH.lib) so I think I'm just missing a step in loading these into LEaP correctly.

I'm using ff99SB because the simulations I'm recreating initially to learn how to deal with these enzyme-ligand complexes used it too. I have seen papers on ff14SB and ff19SB improving on ff99SB however

From: David A Case <>
Sent: 11 January 2021 13:29
To: AMBER Mailing List <>
Subject: Re: [AMBER] LEaP Error/questions.

On Mon, Jan 11, 2021, Sam Walsworth (Researcher) wrote:
>When you load a complex into LEaP using complex = loadpdb ... does that pdb
>file have to be all atoms or just the coordinates of the heavy non-hydrogen

It generally matters very little, since leap will add build in hydrogens in
standard positions if they are missing.

>Also I got fatal errors saying atom does not have a type when I tried to
>create parameters.

You mention "complex": do you have a ligand or other non-standard component?
Look at the "Developing non-standard parameters" at the tutorial tab on the
Amber web page, especially tutorial 2.1 (if you have a ligand.)

...good luck...dac

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Received on Mon Jan 11 2021 - 09:30:02 PST
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