Re: [AMBER] Error in xleap: water molecules

From: Bill Ross <>
Date: Sat, 9 Jan 2021 18:31:13 -0800

"I bet" kind of implies guesswork.Taking a break from this list again,
since I'm in the way.

So, numbering the water residues all 0 it will work the same.

Might be interesting to try.


On 1/9/21 6:25 PM, David A Case wrote:
> 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
> residues.
> I think we need to know more about this particular PDB file to see what is
> going on.
> ...dac
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Received on Sat Jan 09 2021 - 19:00:02 PST
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