Re: [AMBER] tleap neutralization bug?

From: David A Case <>
Date: Fri, 19 Sep 2014 11:45:06 -0400

On Thu, Sep 18, 2014, Gulsevin,Alican wrote:

> 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

The fix that is coming doesn't address this issue. (The fix is just a
convenience: if you don't know how many ions you need to neutralize a system,
tleap will now do a better job of estimating that.)

We may be able to force antechamber to come up with charges that sum exactly
to zero when each charge is truncated to three digits. But it's a little
tricky to actually do that, so don't hold your breath.

> Charge imbalance can cause huge problems at NPT stage

I have not seen this in my own work. It would be interesting to see pointers
to particular examples.


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Received on Fri Sep 19 2014 - 09:00:03 PDT
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