If the torsional parameters are not defined, then you need to do QM
calculation around that torsion to extract/calculate the parameters. You
can check out the following paper for methodology.
"Re-parameterization of RNA CHI Torsion Parameters for the AMBER Force
Field and Comparison to NMR Spectra for Cytidine and Uridine," I.
Yildirim, H.A. Stern, S.D. Kennedy, J.D. Tubbs, and D.H. Turner, J. Chem.
Theory and Comput. 6, 1520-1531 (2010).
Basically, you will do a potential energy surface (PES) scan for
OH-C3-C3-F while keeping almost all the other torsions frozen. Depending
on the system you will use, you might need to use improper torsional
restraints on the system to keep the rings planar. My suggestion would be
to use a real system in the PES scan rather than a model system. Good
luck,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Fri, 21 Jan 2011, Stephane Abel wrote:
> Dear AMBER users,
>
>
> I am trying to build the trifluoroethanol parameters from GAFF force
> field for MD with GROMACS code. For this purpose the parameters in the
> GAFF.dat file given in the ambertools package (v. 1.4). I have defined
> the TFE atome types as follows :
>
>
> [ TFE]
> [ atoms ]
> C1 C3 0.64900 1 <---- C3 is as a Sp3 C
> (correct ?)
> C2 C3 0.09760 2
> O1 OH -0.57850 3
> F11 F -0.23790 4
> F12 F -0.23790 5
> F13 F -0.23790 6
> H21 HC 0.06200 7
> H22 HC 0.06200 8
> H3 HO 0.42150 9
> [ bonds ]
> C1 C2
> C1 F11
> C1 F12
> C1 F13
> C2 O1
> C2 H21
> C2 H22
> O1 H3
>
>
> I can define all the bond and angle parameters. But for dihedral
> parameters, the OH C3 C3 F quadruplet is not present in the
> gaff.dat file.
>
>
> Any advice is welcome
>
>
> Stephane
>
>
>
>
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>
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Received on Fri Jan 21 2011 - 07:30:11 PST
