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

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Feb 9 12:32:42 CET 2006

Hi David

Sounds nice.
I also had to fix several problems with the FF. Especially this 
O2/O-Stuff is nasty. :)
I also tried to generate the termini-files, but the problem is the 
inconsistency of the charges in the BBs of the different AAs.
Maybe that's the reason, why no entries exist. I think, one can't fix 
that problem without calculating the whole FF again.

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


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

David Mathog 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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