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

David Mathog mathog at caltech.edu
Thu Feb 2 21:50:41 CET 2006

Tsjerk A. Wassenaar wrote:
> Hi David,
> Yeah, wouldn't we all want to be able to take arbitrary pdb files, run
> through a black box, fixing missing atoms, residues, deviations from
> conventions, etc, etc.

I'd be happy if pdb2gmx would at least work MOSTLY with the output
of some program.  When it wants protons it apparently only wants SOME
protons.  WHY????

I just tried the WHATIF server and it added a slew of hydrogens that
pdb2gms didn't like. It also turned up a BUG in pdb2gmx. 

1.  Take the output of the whatif server and convert all ' to * in
the nucleic acid section of the resulting PDB file.

2.  Global search and replace OP1->O1P, OP2->O2P

3.  Hand edit (blech, or write a script) to do:
A:  DCYT:  leave H41,H42; remove *H5*,H5*,H4*,H2*,H1*
B:  DGYA:  leave H1,H21,H22; remove *H5*,H5*,H3*,H8,*H2*,H2*,H8
C:  DADE:  leave H61,H62; remove *H5*,H5*,H4*,H3*,*H2*,H2*,H1*,H8,H2
D:  DTHY:  leave H3; remove *H5*,H5*,H4*,H3*,*H2*,H2*,H1*,H71,H72,H73,H6

4.  The bug is that pdb2gmx apparently is not processing DTHY correctly
since it issued no warnings for the hydrogens listed under REMOVE,
whereas it flagged them for DCYT,DGYA, and DADE.

After all that it was still complaining about the missing P,O1P,and O2P
on the 5' end of the DNA (the oligos in the structure were not
phosphorylated).  So turn on -missing to shut that up and then
it blows up in the protein.   Move the DNA parts to after
the protein part and ugh, same deal, Gromacs
version of "protonated" doen't include all the proteins.  For LYS
it has HZ1,HZ2,HZ3 but not any of the others.

Which program has an add SOME protons feature that will make
pdb2gmx happy???


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

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