Re: [AMBER] LEaP Error/questions.

From: Sam Walsworth (Researcher) <"Sam>
Date: Mon, 11 Jan 2021 13:45:18 +0000

Hi David

Yes I have a ligand which it doesn't recognise but it also doesn't recognise any atoms in the amino acids. Essentially the entire system is being flagged as non-standard by ff99SB. I haven't modified any of the amino acid residues in the PDB file so if the atom types are all not recognised by AMBER it sounds like I've missed a preparation/cleaning step.

I'll check out the tutorials also

Thank you for the reply

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 - 06:00:06 PST
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