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 - 03:30:03 PDT
