[gmx-users] Fatal error pdb2gmx

[Paolo Costa]

Dear Gromax users,

I created a new residue of 118 atoms within Amber99 force field. However
when I run the "pdb2gmx" I got many times the following warning: "*WARNING:
Duplicate line found in or between hackblock and rtp entries" *and in the
end I got the following fatal error: "*Atom O10 in residue POM 0 was not
found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea
what the warning means, however I do not understand the fatal error since I
am sure that the Atom O1 is present in the residue I created. In attachment
you can find the .pdb and the .rtp files I created.

Please, can somebody figure out what cause such errors?

Thanks a lot.


Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)