Thank you Jason. Probably, the discrepancy comes from my ligand.
One additional question. How critical is inadequate neutralisation, say 7 instead of 8 Na+?
Regards
George
On Dec 29, 2011, at 4:25 PM, Jason Swails wrote:
> On Thu, Dec 29, 2011 at 5:27 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> This may be a trivial question but any "enlightenment" would be most
>> welcome.
>>
>> tLeap charge COMPLEX gives Total perturbed charge: -7.998000. Yet "addions
>> COMPLEX Na+ 0" produces "7 Na+ ions required to neutralize". Shouldn't it
>> be 8 ions instead?
>>
>> Asking this out of curiosity. Thanks in advance for any answer.
>>
>
> The problem is that the charge is cast as an integer (or supplied to the
> floor() function, I don't know which without looking at the code), meaning
> that any fractional charge is ignored. As close as 0.998 may be to 1, it
> doesn't actually register as a full charge, and as such is not neutralized
> by addions.
>
> It doesn't make much sense to have 0.998 of an electron, so you may check
> why this charge is coming out this way in the first place. Do you have a
> custom residue that you derived charges for? If so, I would suggest
> assigning that 0.002 e-charges somewhere on that residue.
>
> HTH,
> Jason
>
>
>> Regards
>>
>> George
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 29 2011 - 08:00:04 PST
