[gmx-users] OPLS-AA dihedral angles

[Mark Abraham]

MURAT CETINKAYA wrote:
> Hi all,
> 
> I am trying to obtain proper dihedral parameters for  CA-CT-CT-CA  type, 
> which is not in the OPLS-AA database. I have found a set for periodic 
> dihedral type (from AMBER database) but I dont know how to convert that 
> into RB form. GMX Manual does not mention how to convert periodic proper 
> terms into RB form.

Mixing and matching parameters from different forcefields is usually a 
bad idea. Force fields are artificial constructs optimized to reproduce 
some subset of experimental and computational results. There's no reason 
for the CA-CA-CA-CA dihedrals to resemble each other in different force 
fields, and thus no reason for them to interact sanely with the rest of 
each other's force fields. Can you use a whole AMBER force field?

> So, my questions are:
> 
> 1) Can I put periodic dihedral parameters into OPLS-AA database?

Yup. Get out your trigonometry - for values of periodicity below 6, you 
can convert periodic to RB forms, but read the relevant sections of 
chapter 4 and 5 of the GROMACS manuals (and the AMBER documentation!) to 
get sign conventions right.

> 2) If (1) is no, then how can I convert periodic type into RB form? Is 
> there any specific point to consider when using AMBER terms? (e.g. 
> multiplying coefficients by 2)
> 
> 3) Does anyone readily have the CA-CT-CT-CA dihedral parameters :)

Not I.

Mark