Re: [AMBER] LEaP Error/questions.

From: David A Case <>
Date: Mon, 11 Jan 2021 08:29:47 -0500

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 - 05:30:07 PST
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