Quoting Huang Jing <jing.huang8911.gmail.com>:
> One immature way is to add -0.001 e to any atom of .mol2 file and then the
> net charge is zero, if you are disgusted at this non-integral net charge. I
> believe the physical/chemical/biological picture would not be changed with
> -0.001 net charge;
Yes, who cares? ;-) that being said - an error of +/- 0.001 i.e. +/-
0.0010 for a charge accuracy of 1.10-4 (i.e. 0.0001) is _not_ normal
[but particular cases - for instance C(Me)4 i.e. because of chemical
equivalencing] and 'might' reflect something 'wrong' in the charge fit
procedure. For sure we have spent 'some time' on such a problem [even
for C(Me)4], and PyRED
(
http://q4md-forcefieldtools.org/REDServer-Development/) does/should_?
handle that... But once again this was already reported/discussed in
the Amber mailing list.
regards, Francois
> On Sat, Jan 7, 2017 at 8:33 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Azade,
>>
>> > I have a problem similar to here <http://archive.ambermd.org/
>> all/2855.html>.
>> > Unfortunately, I did not find an answer to that inquiry.
>> >
>> > I am using antechamber on a pdb file to create the mol2 file.
>> >
>> > The molecule should be charge neutral and I am using ‘-c bcc –nc 0’
>> flags.
>> > However, the sum of the charges in the output.mol2 generated by
>> antechamber
>> > is not 0.0.
>> >
>> > I also tried ‘-ek maxcyc=0’ flag on several initial.pdb files (point 7,
>> > P.277 of the manual) which all of them lead to a non-zero net charge. The
>> > smallest net charge which I can get is 0.001.
>> >
>> > My question is whether or not this net charge is small enough so I can
>> work
>> > with it or is there is another trick which I can use?
>>
>> If one uses/selects a charge accuracy at 1.10-4 one should get 0.0000
>> as a total charge for a neutral molecule (this is quite basic).
>> If one uses a charge accuracy at 1.10-3 one should get 0.000 as a
>> total charge for a neutral molecule.
>>
>> The problem is not to get 0.001 for a charge accuracy of 0.000 (this
>> error is acceptable); the problem is to get 0.0010 for a charge
>> accuracy of 0.0000: here there is something wrong (because of charge
>> equivalencing?)
>>
>> The problem you underlined was reported mannnny times for antechamber,
>> and was corrected - not corrected?
>>
>> If you use PyRED at RED Server Dev.
>> http://q4md-forcefieldtools.org/REDServer-Development/ this problem is
>> fully handled for whole molecules _and_ molecular fragments whatever
>> is the selected charge accuracy (1.10-4 is the default).
>>
>> regards, Francois
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Sun Jan 08 2017 - 10:30:02 PST
