Hello Charles,
I am attempting to run a docking simulation
similiar to the one published in JACS (2003) 125, pgs 2902-2912. In
the demonstration files, I noticed that the atom numbers in the psf
files and pdb files seem to correlate. When I use pdb2psf, the
resulting output file gives me a psf file that does not necessarily
match ATOM numbers. I have been getting errors trying to run the
simulation using other PDB files - particularly with respect to
loading the coordinates. Is this the cause, and, is there an easy cure?
-Best
Andrew
