[gmx-users] modeling unnatural amino acids

[Erik Lindahl]

Rich McClellan wrote:

> Hi,
>
> I have a peptide composed of unnatural amino acids that I'd like to
> model with GROMACS.  GROMACS (pdb2gmx) is unable to calculate the
> molecular topology of the system and gives an error message stating that
> the residue is not found in the topology database.
>
> Generating the topology file from hand looks daunting so I was wondering
> if somebody has developed a topology database of "other" amino acids or
> have suggestions on the best way to proceed.
>
>         thanks in advance,
>         Rich

Hi Rich,

It's not too difficult to add a new residue to the topology database. 
Have a look in the file ff<name>.rtp, where <name> is the force field 
you are using.

You can probably copy most parts from a standard amino acid that is 
similar to your new one. There are three parts for each residue:

[atoms]
This section maps names found in the pdb file (col 1) to atom types (col 
2), charge (col 3) and charge groups (col 4). Try to have neutral charge 
groups.

[bonds]
Just define the connectivity in the residue. Names prepended with a dash 
("-") refer to atoms in the next residue, if present.

[impropers]
Define the improper dihedrals needed to maintain chirality of the molecule.


That's it - everything else like angles, normal dihedrals, and the 
actual parameters will be generated by pdb2gmx.

Cheers,

Erik