Re: [AMBER] tleap neutralization bug?

From: Gulsevin,Alican <>
Date: Thu, 18 Sep 2014 20:00:21 -0400

Thanks a lot for the effort and consideration. I think it is much more
user friendly for AMBER to round up the charge than to leave it as is
when the difference is as subtle as 0.001 -which again is generated by
antechamber-. This propensity becomes particularly dangerous when one is
not familiar with the system, new users of AMBER that are not
well-informed on how things work, or for people using an automatized
methodology. Charge imbalance can cause huge problems at NPT stage -as
explained in your former answer, and for one thing, trivial reasons are
always the hardest to debug-.


On Thu, 18 Sep 2014 12:44:25 -0400, Jason Swails wrote:
> 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?
> An executive decision was made to consider this a bug worth fixing
> (rather than a legacy 'feature' we need to maintain :).
> So I'm switching my stance from my last response: yes, this will be
> fixed. I've already fixed it in the development tree and just have
> to
> get it tested out a little bit before creating an update.
> All the best,
> Jason

AMBER mailing list
Received on Thu Sep 18 2014 - 17:30:02 PDT
Custom Search