[gmx-users] modeling unnatural amino acids

Erik Lindahl lindahl at stanford.edu
Mon Apr 22 23:50:14 CEST 2002

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:

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 

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

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.



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