Jason,
Thank you very much for your help, especially the script. If I understood
correctly, there are no existing values of partial charge on butane that
are directly applicable to the dihedral scan. I need to do RESP fitting
over a set of conformations to derive the charges. Is that correct?
Best,
Yingjie
On Thu, Jun 26, 2014 at 1:54 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, 2014-06-26 at 12:57 -0500, Yingjie Wang wrote:
> > Hi AMBER experts,
> >
> > As a new learner to AMBER, I just want to study a simple case: the
> > torsional profile of along the C2-C3 bond of n-butane from 0 to 360
> > degrees. I am developing QM/MM methods in Gaussian program where AMBER is
> > an available choice for MM part, but the AMBER96 parameter used in
> Gaussian
> > doesn't specify the partial charges nor the full Fourier terms of butane.
>
> The prototypical "Amber" force fields (Amber94, 96, 99, 03, 99SB, 12SB,
> and 14SB) are designed for proteins and nucleic acids. Small molecules,
> such as butane, are treated using the general Amber force field (GAFF).
> The antechamber program performs the atom typing, and the parameters are
> taken from gaff.dat in the AmberTools distribution.
>
> >
> > The first question is on the RESP charges. As I found in the following
> > literature,
> >
> > Application of RESP charges to calculate conformational energies,
> hydrogen
> > bond energies, and free energies of solvation,
> > Wendy D. Cornell
> > <
> http://pubs.acs.org/action/doSearch?action=search&author=Cornell%2C+W+D&qsSearchArea=author
> >
> > , Piotr Cieplak
> > <
> http://pubs.acs.org/action/doSearch?action=search&author=Cieplak%2C+P&qsSearchArea=author
> >
> > , Christopher I. Bayly
> > <
> http://pubs.acs.org/action/doSearch?action=search&author=Bayly%2C+C+I&qsSearchArea=author
> >
> > , Peter A. Kollmann
> > <
> http://pubs.acs.org/action/doSearch?action=search&author=Kollmann%2C+P+A&qsSearchArea=author
> >
> > J. Am. Chem. Soc., 1993, 115 (21), pp 9620–9631
> >
> > Different RESP charges are assigned to gauche and trans conformation of
> > butane. Does it mean that we cannot scan the whole potential profile
> from 0
> > to 360 degree with the same set of charges? If we can, what vaules should
> > we use?
>
> The charge derivation scheme utilizes conformationally averaged charges
> (that is, multiple conformations go into the fit) and equivalent atoms
> are restrained to all have the same charge.
>
> > The second questions is on the Fourier components of the C-C-C-C bond.
> Are
> > the following third components from PARM99.dat are what we want to use
> > exactly?
> >
> > CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al,
> > 1999
> > CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al,
> > 1999
> > CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al,
> > 1999
>
> This is the term I would use. Note this is the same as the c3-c3-c3-c3
> gaff torsion.
>
> > The third question is on the full MM torsional profile of butane using
> the
> > AMBER program. If I have the correct parameter from the first two
> > questions, I might be able to get the profile just using Gaussian, but it
> > would be ideal to have referenced results from the AMBER program. As I am
> > new to AMBER and has no idea on the detailed specification, can anyone
> give
> > some suggestions or even example inputs on such kind of calculation?
>
> I posted a script that would perform a restrained potential energy scan
> using Amber a bit over 4 years ago. You can download it here:
> http://archive.ambermd.org/201002/0249.html -- you can either use that
> directly to perform a torsion scan or use it as sample input to for
> doing a scan (consult the manual when you have questions about input
> variables and such).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yingjie Wang
Ph.D candidate for chemical physics
Prof. Gao research group
University of Minnesota at Twin Cities
Room 63, Kolthoff Hall
207 Pleasant St. SE
Minneapolis, MN 55455
Cell: (612)-860-1634
Office: (612)-625-5325
Email：wang1710.umn.edu <lsjyppku.gmail.com>
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Received on Thu Jun 26 2014 - 13:30:02 PDT
