From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jul 01 2010 - 05:07:27 CDT
Hello,
This might be more of a CHARMM force-field question, but since I'm more
comfortable in the NAMD community I'll try here first :)
In the CHARMM force-field there are dihedral angle potential functions for
quadruples of atoms.
So, if I'd like to plot the potential function for a rotation around a bond,
then should I sum the potential functions for all possible quadruples around
that bond?
For example if I wanted to plot the potential for the rotation around the
first bond in 2-chloropropanol then should I sum the following terms:
HO Cl
\ /
H -- C -- C -- CH3
/ \
H H
O - C - C - Cl
O - C - C - C
O - C - C - H
H - C - C - Cl x 2 (each with different offset?)
H - C - C - C x 2
H - C - C - H x 2
and in propan just
H H
\ /
H -- C -- C -- CH3
/ \
H H
H - C - C - H x 6 (each with diffrent offset?)
H - C - C - H x 3
Any suggestions about what would be the easiest way to obtain the potential
for rotation around each single bond for every amino acid side-chain?
I'm thinking of either parsing the topology file directly, getting all
combinations of dihedrals and looking this up in the parameter file (a bit
complicated).
Or perhaps I could generate a peptide composed of all the difrent amino
acids, then I have the dehidrals in the psf files, so I just look up all the
combinations in the parameter file (still complicated but not that much).
Perhaps I'm missing something and this is trivial to do in another way?
thank you for your help & best regards,
Ajasja
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