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

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 3 20:47:36 CET 2006

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? 

> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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