[gmx-users] covalent bond lookup table

[Mark Abraham]

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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