[gmx-users] Request for PDB with the same label as in Gromocs topologies.

[David Mathog]

Mikko Hellgren wrote:
> 
> Hi all Gromacs users and developers, I wonder if anybody has pdb files
> for NAD+ (NADH in Gromacs), NADH (NADP) and Retinol (RTOL) with the same
> labels as in Gromacs topologies. This would save me a lot of time in my
> work since the atom names in my PDB for the ligands are different from
> Gromacs atom names, and it would take me a lot of time to figure out how
> to make them consistent to each other. 

Well, not exactly, but this may help.

If you build in the changes I made for 3.3 (from:
ftp://saf.bio.caltech.edu/pub/software/molbio/gromacs-cit-33.tar.gz
)
you can add residue entries for NAD+/NADH/RTOL or whatever in the
residue_name.tbl file to map residue names PDB <-> Gromacs/Amber.
Then add corresponding lines in the atom_name.tbl file to complete the
mapping. This should let you use those molecules in existing
PDB files with existing force field descriptions and import them
through pdb2gmx without hand editing the PDB files.  However, it
will not create the force field descriptions.  And you will need
to figure out for yourself once what the atom name translations
are for each atom in the molecule.  For the PDB side of this
consulting the pdb het_dictionary.txt file may be helpful, from:

  http://deposit.pdb.org/het_dictionary.txt

This file contains all the official PDB atom names and connect records.
(It's almost 10Mb, so better to download it and open it with an editor
than to just click on the above link!)

My code changes are only intended to simplify name translations, they
cannot be used to autogenerate forcefield descriptions.

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech