Dear JiYuan,
> I used MCPB to handle with the metal center of my metalloprotein,I can
> obtain the AMBER prep and frcmod Files for the metal center,I found that
> the sum of the charge with the metal center is 1.00002,
this is normal - this is a rounding off error: this appends when a sum
of several charge values is carried out.
> it caused the
> charge of the complex -4.999980,not a integer.
this is normal
> In order to perform the
> calculation of MMPBSA,I added TIP3PBOX and 5 Na+ ions,but the charge of
> the solvated complex is 0.00002,not zero,
this is the resultant rounding off error; this is normal
> is this status normal?could it
> affect the accuracy and rationality for MD simulation and MMPBSA
> caculataion?
No I do not think so
a trick with rounding off errors is that in some cases (I guess when
the rounding off errors is relatively important - at 10-4 instead of
10-6?) the 'addIons' command of LEaP used to add a wrong number of
counterions if a relatively large rounding off errors was encountered
(5.10-4 for instance?). I know this problem was corrected and it
appeared again and by now I do not know if is is solved. For sure, if
the right number of counterions is added by LEaP this type of rounding
off errors does not matter.
Moreover, the periodic system - if any - should be automatically
neutralized...
R.E.D. III.5 & soon R.E.D. IV automatically correct such a rounding
off errors at an accuracy defined by the user in agreement with (i)
chemical equivalencing and (ii) charge constraints defined required
for the charge fitting step.
regards, Francois
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Received on Tue Feb 21 2012 - 00:00:02 PST
