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

From: case <>
Date: Mon, 6 Aug 2012 21:28:13 -0400

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.


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Received on Mon Aug 06 2012 - 18:30:04 PDT
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