[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS)

Maik Goette mgoette at mpi-bpc.mpg.de
Tue Mar 21 11:51:59 CET 2006

Thanx !

Hopefully, this can be implemented in the next GROMACS version.


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:
> I've been working on table driven translation between PDB
> and AMBER/GROMACS "PDB" files.  That is, getting things that are
> nominally in PDB format into, through, and out of the GROMACS package
> without having to edit PDB files.  Especially structures that used
> DNA and Protein, and so had to use the AMBER FF files.
> For instance in a "PDB" file the same atom might be written:
> (PDB) T:5CM, (GROMACS) THY:C7, or (AMBER) DC5:5CM.  
> The flip side of my changes is that if you encounter new
> residues or atoms the translation tables may need to be edited,
> but that can be done once, versus every time for the PDB files.
> The pieces needed to implement these changes are here:
> ftp://saf.bio.caltech.edu/pub/software/molbio/gromacs-cit-33.tar.gz
> Unpack that from one level above "gromacs-3.3" and it should put
> program files where they need to go.  (If you have local changes don't
> do this, it may stomp on your changes!)  Then follow the instructions
> in AAAREADME_CIT.TXT, which will be in the top level.  In short,
> move the two name translation tables (for residues and atoms) to
> "top", set up AMBER and FF.DAT in "top" as well, and then use
> ./configure, make, and make install normally and the changes should go in.
> Programs that are changed are:
> pdb2gmx:  on my test cases did a good job of PDB -> GROMACS 
> (if no DNA) or PDB -> AMBER (even with DNA).  If protons have
> been added, for instance with "reduce", -ignh is generally needed
> to go to GROMACS but not to AMBER.
> trjconv:  with -dump N -ff AMBER (or -ff GROMACS, the default) now
> exports a PDB file that most programs can read. Generally you 
> will want to export the entire system and use -nowet to remove
> the waters.  If -wet (the default) is used a zillion waters 
> go into the PDB file as ATOM when they should be HETATM.  Eventually
> the program could guess the -ff, but for now you must tell it
> which one you used with pdb2gmx.
> Note that trjconv still uses the default GROMACS classification
> code, as does ngmx and the rest of the GROMACS package.  Consequently
> AMBER residues will typically end up in their own groups since
> these existing routines have no idea what DC5,HIE, etc. are.  But
> trjconv only lets you select a single group to export.  That is why
> you should select system (group 0) and remove the waters (generally)
> with -nowet.
> I do not guarantee that any of this works correctly.  It seems to
> for my test cases, but treat this as an alpha release and proceed
> at your own risk.
> Regards,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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