[gmx-users] covalent bond lookup table

Stefano Meliga 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

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 

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 
be useful.

Can you think of an easy solution?



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