Re: [AMBER] Error in xleap: water molecules

From: Eduardo R. Almeida <>
Date: Sun, 10 Jan 2021 03:02:21 +0000

Dears David A. Case and Bill Ross,

I am sending you a link of this PDB file:
Shared with Dropbox

Thank you for your attention and help.



De: David A Case <>
Enviado: sábado, 9 de janeiro de 2021 23:25
Para: AMBER Mailing List <>
Assunto: Re: [AMBER] Error in xleap: water molecules

On Sat, Jan 09, 2021, Bill Ross wrote:

>I bet the res numbers are being chopped by reading the pdb format, and
>maybe if they were shifted a position after the digits get too many
>amber could handle them.'re just guessing here, and most guessing wrong. Amber
internally increments the residue number whenever the residue number in the
PDB differs from the one before it, or when a TER card is read. Amber's
residue numbers are not limited by the four-character limit. And there are
tons of systems handled by Amber that have very large numbers of atoms and

I think we need to know more about this particular PDB file to see what is
going on.


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