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
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