Re: [AMBER-Developers] non-neutral ethane from antechamber

From: Crowley, Michael <>
Date: Fri, 3 Feb 2012 12:55:56 -0700

Hi Francois,
Thanks a lot for your interest, I see your points.
I am fine with lower precision, but do not understand what antechamber is
doing with the lower precision. The charges do not make sense compared to
the higher precisions, they are not rounded off numbers, they are
different and don¡¯t sum to zero, not even close. From what I see, the
first column should have -0.0939 and 0.0313. Even with the -0.0941, the H
charges should be 0.0314 not 0.0317. Even with two digits of precision,
the charges should be -.094 and .031 with a sum of 0.001, half of the
antechamber sum/error.
  formats from sqm
  f14.3 f14.4 f14.5 f14.8
-0.094100 -0.093900 -0.093890 -0.093887
  -0.094100 -0.093900 -0.093890 -0.093887
 0.031700 0.031300 0.031300 0.031296
 0.031700 0.031300 0.031300 0.031296
 0.031700 0.031300 0.031300 0.031296
 0.031700 0.031300 0.031300 0.031296
 0.031700 0.031300 0.031300 0.031296
 0.031700 0.031300 0.031300 0.031296
 0.002000 0.000000 0.000000 0.000001

Does that make sense, or am I still wanting too much from these programs?
At least for this case it looks to me that just changing the precision by
one or two in the printout is a workaround if not a real solution.

Best wishes,

Michael F. Crowley, Ph.D.
Principal Scientist, Biomolecular Sciences Division
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
303-384-6345 office
303-887-0149 cell

On 2/3/12 2:13 AM, "FyD" <> wrote:

>Dear Michael,
>Considering ethane & n-alkanes more generally:
>Please, see
>The problem you report is related to rounding off errors: Rounding off
>errors are really a problem... If the accuracy requested in the
>program output is at 6 digits as in the RESP output, the max. error
>that is accumulated is +/-Y.00000X (Y is an integer & X is around 6-7
>from our tests). But, here, who cares ;-) as X.10-6 remains a small
>Then, if the accuracy requested is at 4 digits (Cornell et al. force
>field) the rounding off errors becomes +/-Y.000X, which remains
>acceptable; this becomes the pain if the accuracy requested is at 3
>digits (GLYCAM) or even 2 digits (CHARMM_?).
>Then, an additional problem is that when correcting these rounding off
>errors, chemical equivalencing should not be broken; at 10-6, it does
>not really matter once again I guess: but what about for an accuracy
>of 10-3? We have developed an algo. related to this rounding off
>errors in R.E.D. We should released it in soon in R.E.D. Server first.
>The idea of this algo. is to automatically correct rounding off errors
>in the context of a force field topology database generation (large
>set of FF libraries) in agreement with (i) the charge accuracy
>requested by the user, (ii) chemical equivalencing required in MD
>simulation, and (iii) the constraint values requested during the fit.
>regards, Francois
>> I wonder if there is something wrong with either my approach or with the
>> antechamber process.
>> Something as simple as ethane gives charges that do not add to zero
>> (+0.00200).
>> input pdb attached and output mol2 file.
>> This is the command:
>> antechamber -i ethane.pdb -fi pdb -o ethane.mol2 -fo mol2 -c bcc -s 2
>> Motivation:
>> We use Amber, Namd, and charmm a lot imoving between programs for
>> different purposes on the same system and it is pretty important that
>> program is getting the forces right for each force field.
>> In an effort to test force fields in each program (we are also testing
>> gromacs and LAMMPS, though we don©öt use them much), we are making some
>> simple test cases.
>> This test is meant to test amber ff (gaff in this case) in the other
>> programs and compare results to amber.
>> We create simple molecules in the amber process and then run them in the
>> other programs converting input as needed.
>> Problem starts with antechamber, giving a non-neutral alkane.
>> If I manipulate the charges to be neutral, we can continue, but I think
>> antechamber should do that.
>> Am I expecting too much? Is the collective wisdom on antechamber that it
>> is imprecise enough that manipulating the charges is no worse than what
>> you are getting anyway?
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