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

Ken Rotondi ksr at chemistry.umass.edu
Fri Feb 3 15:00:13 CET 2006


Unfortunately computers are not crazy, just very inflexible when 
executing commands.

It sounds like your hydrogen data base file (ffXXXX.hdb) is not 
complete. Are the warnings (without -missing, I really wouldn't use 
that unless you are sure that you want to use incomplete molecules) of 
the type:

WARNING: atom H62 is missing in residue ADE XXX in the pdb file

If that is the case you need to modify your .hdb file to include the 
DNA hydrogens.

Good luck,


If it doesn't specify
On Feb 2, 2006, at 5:36 PM, David Mathog wrote:

> More progress, sort of.
> By changing C7 -> C5M in the DTHY records I finally managed
> to get pdb2gmx -ignh -missing to run to completion.
> That said, it does not appear to have worked correctly.
> 1.  None of the DNA is protonated.
> 2.  The protein is protonated
> which is craziness, it should be one way or the other.
> 3.  There were 3 long bond warnings right after "Making bonds...".
> However I cannot figure out why they are there since the
> corresponding atom positions in the gmx output file don't correspond
> to atoms that make bonds in the rtp file.
> What do the position numbers in the long bond message refer to?
> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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