On Mon, 2014-02-24 at 17:22 +0000, Mele N. wrote:
> THe problem is I can' t see anything because I don' t get any output file. The mdcrd that I get at the end is empty.
> I can't pass any step during the heating.
I'm confused. You kept giving the 'equilibration' input file yet you
say the heating stage was the one having problems? If the heating stage
went fine, look at the output files from that step to see if anything
looks wrong (the "checkoverlaps" command in cpptraj can help when
looking for close contacts).
If the heating stage didn't work, look closely at the result from the
minimization step. I've also seen this type of error occur when the box
information is set incorrectly (e.g., did you build an octahedron box
with packmol but set your box to an orthorhombic shape in tleap? vice
versa?).
If the box information is wrong, then periodic images will most likely
overlap strongly and these errors are sure to occur.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 24 2014 - 10:00:04 PST
