Re: [AMBER] tleap neutralization bug?

From: Jason Swails <>
Date: Tue, 16 Sep 2014 13:25:21 -0400

On Tue, 2014-09-16 at 11:54 -0400, Gulsevin,Alican wrote:
> Begging the first question, the neutralization bug itself, would you
> consider fixing this problem in one of the following updates or
> versions, or is it something implemented by the method the system
> charges are calculated and cannot be fixed?

It appears that what Amber does is truncate the charge (possibly because
it casts to an integer). It could be changed to allow for some kind of
tolerance pretty easily, I think.

I'm a little wary of changing tleap's behavior that has been this way
for decades. In my experience, this problem can be fixed just by making
sure that any ligand residues have a full integer charge.

I'll raise this for discussion on the developer's list to get some
ideas. It may be that we can do something like add a keyword that
allows someone to specify a tolerance that would trigger the addition of
one more ion so there's an easy way of getting the behavior you want
without modifying existing behavior.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Sep 16 2014 - 10:30:02 PDT
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