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

David Mobley dmobley at gmail.com
Wed Feb 8 01:32:40 CET 2006

Amber FF is maintained by the Pande group so you could ask them. But
it hasn't been out particularly long, so I wouldn't be too terribly
surprised if no one has made these yet.


On 2/7/06, David Mathog <mathog at caltech.edu> wrote:
> Well I'm getting closer to "automatic" pdb->gmx but it's still
> more of a slog than it should be.
> 1.  Run raw.pdb file through "reduce -BUILD" -> input.pdb
>     (This puts on all required protons except, alas, for the ones
>     at the N termini).
> 2.  Run raw.pdb through "whatif".  Copy the 3 lines for the 3 N
>     terminal hydrogens into the first Amino acid residue (per chain)
>     in input.pdb.
> 3.  Use modified Amber ff (O -> O2 for all THY residues) and add
>     that to the first position in FF.dat.
> 4.  Run  pdb2gmx  (my own patched up version that automagically
>     changes residue and atom names for Amber, to be posted for your
>     use soon).
> The pdb2gmx runs successfully.  The amount of manual cut and pasting
> has been reduced from a ton to just three lines.
> Unfortunately pdb2gmx won't by itself put on all the hydrogens
> Amber wants so specifying -ignh or feeding in raw.pdb directly doesn't work.
> The carboxyl end is wrong of course, since even if there's an OXT
> in the PDB file nothing useful shows up in the output gro file.  In
> most cases it shouldn't matter much.
> The nucleic acid 5' end must be a OH, since the 5' models in the Amber
> ff set are all like that.
> The ASP/ASPH/GLU/GLUH interactive stuff works and properly ends up
> as the Amber ASP/ASH/GLU/GLH.
> Ideally it would be nice if pdb2gmx could generate the N and C termini
> all by itself.  It looks like "all" that's needed for that are -n.tdb
> and -c.tdb files.  However I don't know yet how to write those.  Does
> anybody have these already for the Amber FF files?
> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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