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 Fri Sep 24 2010 - 12:00:04 PDT
