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)
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