Re: [AMBER] antechamber parameter file issues?

From: Dean Cuebas <>
Date: Sat, 14 Jan 2012 13:37:22 -0600

In my humble opinion, the most important consideration for correct charge
derivation is that the conformation of (especially) flexible molecules is
forced to be as extended as possible to prevent any intramolecular
interactions (H-bonding) that would corrupt the charge fitting method (the
documentation to Openeye¹s Quacpak clearly quotes Bayly in this
regard...). The simplest way to achieve this is use a program like VegaZZ
to assign charges using their SP4 FF then simply change the signs to be
all positive or all negative. Then use the SP4 FF to minimize the
structure. Since all atoms will repel each other, you will (always?)
achieve the most extended conformation. Then use MOPAC with AM1 to
minimize that structure, and then send it to antechamber. My gut feeling
is that the inconsistent use of the most extended conformations is much
more detrimental to accurate charge derivations than any advantage sqm
might have over MOPAC for assigning the AM1BCC charge.

Without knowing if your structure is highly flexible, it's hard to know if
what I discussed is relevant to your particular situation or not.

At the end of the Ambertools 1.5 it states that for AM1-BCC charges for
585 drug molecules, MOPAC and sqm give essentially similar charges for all
the cases and the average charge difference is 0.005. So what are the
advantages to sqm over MOPAC for AM1-BCC, since there appears to be tight
convergence issues with sqm?

Dr. Dean Cuebas, Associate Prof of Chemistry, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
On 1/13/12 8:46 PM, "case" <> wrote:
>On Thu, Jan 12, 2012, Thomas Pochapsky wrote:
>> Thanks to Ben for your help; antechamber in AmberTools 1.5 is running
>> fine, the sustiva example works.  Now I am trying to get it to work
>> for my molecule.  I am trying to parameterize a macrocyclic lactone
>> antibiotic for Leap, and based on the ATOMTYPE.INF file, the atoms are
>> being identified and bonded correctly, but the antechamber run fails at
>> the sqm step. sqm.out says that there is no convergence in SCF after
>> 1000 steps.
>Can you post the pdb (or other) input file you are using?  We need to see
>why sqm is sometimes failing to converge.  This sort of thing sometimes
>happens when the initial geometry is no so good--not your fault, since our
>procedure ought to be insenstive to that.
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Received on Sat Jan 14 2012 - 12:00:03 PST
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