AMBER Archive (2008)

Subject: Re: AMBER: Antechamber/mopac am1-bcc charge

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jun 26 2008 - 13:27:10 CDT

It is true that partial charges should depend on the environment. As a
matter of fact, different HF/6-31G* RESP charges are produced for different
conformations (of course not significant different). However, in MM
calculations using an additive force field, only one set of charges is used.
This set of charges should be "general" and "good" for all the conformations
sampled by MD or minimization.

How to generate such kind of charge? In AMBER, for standard aminio acid and
nucleic acid residues, the charges were derived with RESP using multiple
conformations. Since Mulliken charges are less conformation dependent, one
may get such kind of "general" charges using only one conformation. From
this aspect, we say it is an advantage.

Best

Junmei

On Thu, Jun 26, 2008 at 12:29 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> On Thu, Jun 26, 2008 at 4:33 PM, Junmei Wang <junmwang_at_gmail.com> wrote:
> > Hi,
> > The bcc parameters are same and the final am1-bcc charges depend on which
> > am1 package to be used. However, I don't think the difference of charges
> of
> > Cl- is that significant. One advantage of am1-bcc over resp is that it is
> > less variant for different conformations since am1-mulliken charges are
> > pretty conformation independent.
>
> That lesser dependence of partial charges from the conformational
> status (if this is what you really meant) is interesting. However - as
> a devil's advocate - is that really an advantage? I wish you reassure
> me that it is an advantage. I always thought that it is normal for the
> partial charges to depend on the environment, be that also the
> conformational status itself. We are in the hot season, may be I can't
> rightly grasp what you wrote. Presently, I see that independence from
> the conformation as illusory, thus a disadvantage Sincerely, however,
> I hope I am wrong.
>
> francesco pietra
>
> >I think bcc parameters were derived using
> > the mopac package.
> >
> > Best
> >
> > Junmei
> >
> >
> > On Thu, Jun 26, 2008 at 1:21 AM, Dong Xu <d1xu_at_ucsd.edu> wrote:
> >>
> >> Hi Junmei,
> >>
> >> Thanks for your response. I installed ambertools and tested am1-bcc with
> >> mopac6. When comparing the output files of am1-bcc charge calculations
> from
> >> divcon and mopac for the same molecule, it seems they came to different
> >> optimized geometries and final electronic energies: -34543.95016086 EV
> >> (divcon) and -34945.38044 EV (mopac). The charges are thus different as
> >> well, e.g. a Cl atom has -0.00595 (divcon) and 0.012900 (mopac). So my
> >> questions are, How to reduce this type of variations in am1-bcc charge
> >> calculation and how much effect does it have on the protein-ligand
> >> electrostatic interaction energy estimation?
> >>
> >> Thanks,
> >>
> >> -DX
> >>
> >> On Wed, Jun 25, 2008 at 3:44 PM, Junmei Wang <junmwang_at_gmail.com>
> wrote:
> >>>
> >>> I would like to recommend you to use antechamber in AmberTools. Mopac6
> is
> >>> included in the package and you simply specify "-c bcc" to calculate
> am1-bcc
> >>> charges. For example antechamber -fi mol2 -fo mol2 -i input.mol2 -o
> >>> output.mol2 -c bcc
> >>>
> >>> Best
> >>>
> >>> Junmei
> >>>
> >>> On Wed, Jun 25, 2008 at 5:09 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I downloaded and compiled antechamber-1.27 and noticed that divcon is
> >>>> replaced by mopac6. Could anyone let me know the procedure and command
> to
> >>>> calculate am1-bcc charges using antechamber and mopac?
> >>>>
> >>>> Thanks,
> >>>>
> >>>> -DX
> >>>
> >>
> >
> >
>
>
>
> --
> Dr Francesco Pietra
> Professor of Chemistry
> Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
> Palazzo Ducale
> 55100 Lucca (Italy)
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