From: Sijia (Scarlett) Dong (sijiadong.nature_at_gmail.com)
Date: Mon Aug 12 2013 - 18:55:33 CDT
Dear NAMD users,
I'm using the method on this page:
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node34.html#SECTION000973 to
restrain one of the dihedral angles in a customized residue in my protein.
The relevant lines in my configurations file is:
-------------
freeEnergy on
freeEnergyConfig ret_urestraint
-------------
And ret_urestraint is a file with this content:
-------------
urestraint {
dihe (MAIN, 296, C19) (MAIN, 296, C18) (MAIN, 296, C17) (MAIN, 296, C16)
barr=10000 ref=-157.69
}
-------------
Here is the problem: I have tried "barr" value from 0 to 10000 when I do
minimization on the protein, but the dihedral angle I want to restraint is
always around -161 or -162 deg which is not close to my reference angle.
There is no much trend relating the barr value and the angle I'm getting
except that when barr=0 it is -162 deg which is the same as not using the
restraint. I'm using Amber force field.
Does anyone know what I have done wrong to make the dihedral angle not
getting closer to the reference angle? Are there other parameters I should
be setting as well to make the restraint work? Is there a limitation
related to this method such as it doesn't work with Amber force field?
I'm not using the harmonic restraint here because I want to use a method in
NAMD that has a equivalence to one of the LAMMPS restraining method to
restrain the dihedral angle. The LAMMPS "fix spring" method doesn't work in
the way the NAMD's harmonic restraint works, so I find this method which
seems to be similar to LAMMPS' "fix restrain". If someone knows other
methods that can achieve my purpose, I greatly appreciate it too!
Thanks a lot!
Scarlett
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