Re: [AMBER] non integer charge in antechamber generated mol2 file

From: Raik Grünberg <>
Date: Wed, 8 Aug 2012 13:41:14 -0400

Hi David,

On Mon, Aug 6, 2012 at 9:28 PM, case <> wrote:
> On Sat, Aug 04, 2012, Raik Grünberg wrote:
>> I have used antechamber and parmchk to create a mol2 and frcmod file
>> for a small organic protein ligand with a charge of -1. The original
>> coordinates were extracted from the PDB and hydrogens added with
>> Chimera.
>> I then run:
>> antechamber -i in.pdb -fi pdb -o out.mol2 -fo mol2 -c bcc -nc -1&
>> followed by:
>> parmchk -i *mol2 -f mol2 -o out.frcmod
>> All seems to have worked and sqm.out reports a total charge of:
>> > Total Mulliken Charge = -1.000
>> In reality though, the charges of the mol2 file add up to:
>> -0.996001
>> (In fact, the charges in the output mol2 are different from the sqm.out.)
> This is expected: the sqm.out file has Mulliken charges, whereas the mol2 file
> has am1-bcc charges, which start with the AM1 Mulliken charges, and then
> modify them.
> Currently, the sqm program only prints Mulliken charges to three digits after
> the decimal place, which can lead to normalization errors. You could try to
> modify sqm to print out more digits and see if that helps. (Look around line
> 47 in $AMBERHOME/AmberTools/src/sqm/qm2_print_charges.F90.

Thanks for the hint. I have never programmed in Fortran so i just made
a guess and changed
line 43 from:
        write(6,'(" ",i5," ",A2," ",F14.3," ",F14.3)') i, &
        write(6,'(" ",i5," ",A2," ",F14.6," ",F14.6)') i, &

and applied the same change to line 47 so that it now reads:
        write(6,'(" ",i5," ",A2," ",F14.6)') i, &

... and recompiled everything and re-run antechamber.

Unfortunately, that didn't make any difference. The new mol2 file is
identical to the old one.

I have never worked with the Amber code base but if you want me to try
something else, I can give it a quick shot. Otherwise, if you have a
bug tracker somewhere, I can file a bug together with the input


> ....dac
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Raik Grünberg
AMBER mailing list
Received on Wed Aug 08 2012 - 11:00:03 PDT
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