[gmx-users] Re: converting pdb to gmx successfully

David Mathog mathog at caltech.edu
Fri Feb 10 17:09:27 CET 2006

> The problem with the terminal DNA is, that the O5' and the O3' have to 
> be renamed into O5T and O3T, respectively.

Ah, I see, according to the PDB standard those atoms are
supposed to be marked that way.  The PDB file I'm working on at the
moment just used O5* and O3* for these atoms, so I had not yet
run into this.  I will add some code to convert those names to
the atom names that the FF files expect.

One really odd thing I've found is that for DNA pdb2gmx will add
hydrogens using the Amber FF files, but perversely, it won't when using
the first (in the default FF.dat) Gromacs FF.  However in the same PDB
the Gromacs FF it does put the hydrogens on the protein.


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

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