I'm not sure what is going wrong.
I can successfully build the inpcrd and prmtop for a protein-nucleotide
complex (with and without MG+2) without tip4pew. (nucleotide parameters via
antechamber).
However, when I solvate with TIP4PEW (including the frcmod.ionsjc_tip4pew
and without MG I get the following message:
Could not find bond parameter for: EP - OW
prior to this I also get the message:
(using default radius 1.500000 for EPW)
Using MG (and the parameters from
http://archive.ambermd.org/201202/0429.html)
i get the same thing plus:
1-4: angle 19745 19751 duplicates bond ('triangular' bond) or angle
('square' bond)
can someone point me in the right direction as to what is wrong? Did I
miss something when creating my files in antechamber?
thanks,
Jonathan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 07 2013 - 06:00:08 PDT
