Stefano Meliga wrote:
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
Atom1 Atom2
1 2
1 3
...
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
formula.
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?
Not really. Forcefields select bonded interaction functions based on the
types of the atoms involved. There's no explicit consideration of the
formal "bond number", except inasmuch as some atom types never
participate in double-bonding. sp2 carbons (tend to?) have different
types from sp3 carbons. Perhaps you could infer the kind of bond from
the atom types and/or the stiffness of the bonded potential. You would
still have to have a script parse the atom types and bonds described in
a .top file, look up the ff???bon.itp file and use that data to look up
your own tables. You could also get the data from a script processing a
gmxdump of a .tpr file.
Mark
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
be useful.
Can you think of an easy solution?
Thanks,
Stefano
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