Thanks.
Now I can fix this rounding error.
Bongkeun
Quoting FyD <fyd.q4md-forcefieldtools.org>:
> Dear Bongkeun,
>
> I misunderstood your first email; I thought your error was .01...
>
> ".001" is more understandable: your molecule is large with a bunch of
> atoms being chemically equivalent. Imagine if you have a rounding off
> error of +.0001 for nine hydrogens being chemically equivalent, your
> rounding off error becomes .0009 i.e. close to .001
>
> I would manually correct some partial charge values; adding -.0001 for
> all these chemically equivalent atoms (indeed, LEaP (addion command)
> used to add bad numbers of counterions when the total charge of a
> charged molecule was not near neutrality; this bug was corrected if I
> remember; may-be twice even).
>
> You might also read a message available in R.E.DD.B. about rounding
> off errors:
> http://q4md-forcefieldtools.org/REDDB/error.php
> "Corrections carried out the September 1st, 2009 (Paris time)
> -1- Total charge corrections of some force field libraries for the
> "F-73" up to "F-82" R.E.DD.B. projects"
>
> regards, Francois
>
>
>
>> I made this prepi file from the following procedure.
>>
>> 1. generate mol2 file from the monomer pdb file.
>> antechamber -fi pdb -fo mol2 -i ch3.pdb -o ch3.mol2
>>
>> 2. Generate residue topology file LIC_bcc.prepi directly from ch3.mol2
>> to use AM1-bcc charge and amber atom types.
>> antechamber -fi mol2 -fo prepi -i ch3.mol2 -o LIC_bcc.prepi -j both -c
>> bcc -rn LIC
>>
>> I checked the output files after the number 2 and found
>> ANTECHAMBER_PREP.AC and ANTECHAMBER_AM1BCC.AC files have the total
>> charge 0.001.
>>
>> I attached mol2 and above two output files.
>> Thanks.
>> Bongkeun
>>
>> Quoting James Maier <jimbo.maier.gmail.com>:
>>
>>> Bongkeun,
>>>
>>> Do you know how I can adjust the number of significant figures when
>>>> antechamber generates charges?
>>>
>>>
>>> I am not sure how to do this.
>>>
>>>
>>>> Or do you want me to simply adjust the
>>>> charge distribution on this prep file?
>>>>
>>>
>>> I think it would be preferable to regenerate the charges rather than modify
>>> the file by hand, as where the changes need to be made may not be obvious.
>>> How exactly to accomplish this depends on how you originally fit the
>>> charges.
>>>
>>> What method did you use (e.g., AM1-BCC, RESP...)? Providing some of the
>>> intermediate antechamber files, notably the inputs to whatever charge
>>> program you used and the output ac file with charges, may help someone to
>>> assist you further.
>>>
>>> James
>
>
>
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Received on Sat Sep 25 2010 - 10:30:03 PDT
