Hi ,
I am trying to repeat pKa calculation tutorial with Thermodynamic integration tutorial (Amber tutorial A6-section 1 and 2) using pmemd, but after explicit solvation of the molecule.
My step 1 output file gives me an error "Coordinate resetting (shake) was not accomplished within 3000 iterations ". The ntc and ntf are both set at 2.
I can't figure out where this error is coming from. Attached is the zipped folder containing the prmtop, inpcrd, the mdin and the output file.
I would really appreciate help regarding this matter.
Thanks
Roma
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Received on Wed Oct 04 2017 - 13:30:02 PDT
