[gmx-users] question of improper dihedral of opls aa

[Justin Lemkul]

On 12/17/12 5:51 PM, Tom wrote:
> Dear Gromacs Users,
>
> I created a new residue on aminoacids.rtp file
> and assigned improper dihedral after [ bonds ], for example
>
> [ impropers ]
>        C2    H      C3     S1
>
> Then I want to add the parameters of this dihedral angle potential
> onto ffbonded.itp
>
> I know how to assign dihedral. Dihedral can be assigned with
> these 4 atom types with the format as the follow
>    Br     C      CB     CT      3      0.00000   0.00000   0.00000   0.00000
>    0.00000   0.00000 ; acyl halide
>

That's a proper dihedral, using a Ryckaert-Bellemans function.

> *But the format of improper dihedral potential is not clear to me.*
> *Can anyone help with the format? How to type these parameters
> on ffbonded.itp ?*
>

Check the existing entries in ffbonded.itp.  It's the next [dihedraltypes] block 
with #define statements for the impropers.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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