[gmx-users] covalent bond lookup table
smeliga at gmail.com
Wed Jun 17 16:10:37 CEST 2009
Dear Gromacs users,
I need to produce a list of the covalent bonds of my protein structure
in the format:
Atom1 Atom2 binding energy
1 2 50 kcal/mol
1 3 150 kcal/mol
The binding energy is not the potential calculated by gromacs' force
field but the diatomic binding energies available in the literature
I actually already have a list of the covalent bonds like this
and a table with the binding energies of each bond type like this
bond type binding energy
C-C 150 kcal/mol
C=C 200 kcal/mol
C-H 100 kcal/mol
but, in order to create such file, I'd need to build a script that scans
my pdb looking for the atom types and working out whether in between
there's a single or double bond according to the aminoacid's chemical
Thus, I was wondering if Gromacs can perform any operation to make my
work less painful.
Is there a command or an option able to output a similar file?
It would be already of great help to have a simple lookup table like this
Atom1 Atom2 single-or-double-bond?
1 2 single
1 3 double
I took a quick look to the files ffoplsaa.* but I couldn't quite find
what I was looking for. Maybe the field "name" of the *.itp file could
Can you think of an easy solution?
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