Re: [AMBER] A bug with unperturbed charge during tleap processing

From: James Starlight <>
Date: Thu, 3 Aug 2017 15:38:34 +0200

The problem might be here
Checking Unit.
FATAL: Atom .R<PHE 299>.A<OXT 21> does not have a type.

and in the final topology for the last residue I have charge of OXT
-0.8 like for O which seems not reasonable...

Its strange that I have obtained such atom names from pdb4amber --reduce
but OXT has been present in MODELLER pdb


2017-08-03 13:55 GMT+02:00 David A Case <>:
> On Thu, Aug 03, 2017, James Starlight wrote:
>> The file contained 1 atoms not in residue templates
> I'd suggest tracking down the source of this message.
> Beyond that, this is not something that can be readily debugged via email.
> You report that just removing water molecules changed the net charge of your
> system. It seems clear that something else actually changed, but only you
> can find out what that is.
> Start with a very small protein/peptide (or with just a box of pure water).
> Repeat your procedure, in order to generate the simplest example tha exhibits
> the behavior you see.
> The "summary" command of parmed is a simple way to look at net charges, and
> you can print individual atom charges in that program as well.
> ....dac
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Received on Thu Aug 03 2017 - 07:00:02 PDT
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