[gmx-users] OPLS-AA dihedral angles
Mark.Abraham at anu.edu.au
Fri Apr 20 02:14:55 CEST 2007
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 :)
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