Hello,
I've written a new parameter file for nucleic acid structure
calculation, with a focus on RNA.
I have problems with the angles around the phosphate atom (in the
backbone of course). My question is: would it be possible to formulate
angles as restraints instead of parameters, so it would be very similar
to the dihedral angle restraints.
flags exclude * include cdih {*So dihe from the parameter-file is turned
off, and the dihedral restraint forcefield turned on *}
flags exclude * include cang {*similar but with angles*}
Why do I want this ?
I want to allow a certain range around the angle, which is not marked as
violation. But this holds only for the angles involving phosphate atoms.
So:
restraint angles
assign (resid $1 and name O3') (resid $2 and name P )(resid $2 and name
O5') -50.00 40.00
end
Thanks in advance,
Ramon
--
R.M. van der Werf
E-mail: R.vanderWerf at nmr.ru.nl
Radboud university of Nijmegen
Dept. Biophysical Chemistry (NMR)
