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

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 2 22:23:25 CET 2006

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

I understand your frustration but this is a tricky problem. There are 
four very common naming schemes for hydrogen atoms in proteins. AFAIK 
none of the programs used for NMR refinement complies with the IUPAC 
naming. What is needed is some kind of heuristic algorithm that analyses 
a whole protein, and from that determines which naming scheme is used, 
and from there converts all names to a standard (preferably the IUPAC 
one). However, it is not at all unconceivable that you download a 
protein from the databank, modify it with a program that modifies a 
sidechain and adds in another naming scheme for just that sidechain, 
making the mess complete.

If we tried to implement an omniscient pdb2gmx, there is the risk  that 
it would misinterpret the input and quietly change the chirality of some 
of your amino-acid side chains... The option to toss all the hydrogens 
and add them back is much more robust. Moreover, if you are going to do 
dynamics than the position of the hydrogens will change considerably 
within a few fs, so in my opinion their starting positions are close to 
useless, and idealised positions as generated by pdb2gmx are probably as 
good an approximation as any.

Personally I have close to no experience with DNA work, but there is now 
an OPLS and an AMBER implementation available for GROMACS that should be 
able to treat DNA. I haven't followed the beginning of this thread, but 
it should be possible to use DNA, however probably not without the -ignh 

> 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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