Hello,
A couple of comments:
1. All gaff atom types are lower-case
2. Are you building an amber topology file? I'm not familiar with using an
Amber package to set up a gromacs simulation.
3. If you are creating an amber topology file and converting it later, you
should add missing parameters to an frcmod file rather than directly editing
gaff.dat.
4. Not all parameters for all molecules will exist in gaff.dat. You can use
parmchk to see if any generic terms match the dihedral you're looking for
(i.e. using X as wild-cards for the 1,4 groups).
5. If any are missing, you'll need to determine what those are (i.e. by
comparing to quantum results) and put them in the frcmod file.
Good luck!
Jason
On Fri, Jan 21, 2011 at 9:51 AM, Stephane Abel <Stephane.Abel.cea.fr> 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
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 21 2011 - 07:30:07 PST
