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

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Feb 6 13:11:55 CET 2006

David, that's obvious...;)

Nevertheless, I tried to discuss the topic half a year before.
So, just do it again, now.
What I did to solve the problems, is just renaming everything properly.
Maybe it's a good idea, if we would use a standardized naming for the 
ff-file-entries. I think, there is no need of changing code.
Its easy for pdb2gmx to distinguish between RNA and DNA, if the bases 
are named e.g. DA for DNA-Adenine and RA for RNA-Adenine and so on.
Again, I offer to send my modified files to anyone, who needs them.
pdb2gmx should go through them without a problem, if the PDB-file 
entries are named the correct way. Also the protonation is done the 
correct way.


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 van der Spoel wrote:
> David Mathog wrote:
>> I do a lot of maintenance programming so I figured it wouldn't
>> be too hard to hack up pdb2gmx to handle DNA or RNA (but not
>> both) properly.  Turns out that assumption was half right.
>> It was easy to modify it so that it automagically converted
>> ACGT to DADE (etc) and O1P->OP1, and O2P->OP2.
>> But it still wouldn't put any hydrogens on the DNA.
>> Finally I tracked it all the way through the code until I discovered
>> that _none_ of the hdb files that come with gromacs contain info
>> for nucleic acid hydrogens.
>> Consequently the routine read_h_db in h_db.c couldn't
>> find any relevant data and then search_h_db couldn't match DCYT etc.
>> because no relevant info had been read in.
>> Presumably somebody has an hdb file for nucleic acids? 
> Yes:
> http://folding.stanford.edu/ffamber/
>> Also can somebody please explain why Gromacs ships without this info
>> in the hdb files????
> That's the easy bit: the force field files for gromos are converted 
> automatically, but the hdb info was entered manually. Since none of the 
> gromacs developers has done any DNA work, we didn't bother. That's 
> right, we did not want to spend time on something we weren't going to 
> use. No warranty to be fit for any purpose you know.
> However the amber force field from Stanford should have a correct hdb file.
>> Thanks,
>> David Mathog
>> mathog at caltech.edu
>> Manager, Sequence Analysis Facility, Biology Division, Caltech
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