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

[David Mathog]

David van der Spoel wrote:
> I haven't followed the beginning of this thread, but 
> it should be possible to use DNA, however probably not
> without the -ignh  option.

I just tried -ignh.  It now warns about every H atom listed in
the pdb file (which were the proper ones as far as it was concerned
prior to -ignh) and than throws a fatal error.  It also says
to use -missing to run it anyway.  I take it from your post that
-ignh is supposed to ignore incoming proteins and put on its own???

I'm I nuts or shouldn't -ignh imply "Don't warn/stop on
'missing' H atoms"?

It shouldn't be necessary to add -missing to work around this since
it will mask any real problems elsewhere in the PDB file.

Thanks,

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