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

[David Mathog]

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????

Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech