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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Received on Thu Jun 26 2014 - 12:00:03 PDT
