Hi, I'trying to set up a protein for molecular dynamics simulation.
Following advice from Amber11 manual : (igb=2 and 5) are newer, but
appear to give significant improvements and are recommended
for most projects (certainly for peptides or proteins). I decided to
include "set default PBradii bondi" when preparing my files using
tleap. The simulations worked fine before I tried this extra PBradii
stuff, but now sander and pmemd.cuda aren't even running. As soon as I
type the input line, an error comes out on screen. This is what comes
out for pmemd.cuda:
At line 301 of file prmtop_dat.f90 (unit = 8, file = 'protein.prmtop')
Fortran runtime error: Bad value during integer read
And this is what comes out for sander:
At line 500 of file _rdparm.f (unit = 8, file = 'protein.prmtop')
Fortran runtime error: Bad value during integer read
Any help on the problem would be appreciated.
Thank you
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Received on Thu Oct 20 2011 - 21:30:03 PDT
