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

[David Mathog]

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