Dear Jason
Many thanks for your email and reply. I set the igb=6, the problem was fixed.
Thanks a lotMaryam
On Wednesday, 10 February 2016, 16:14, Jason Swails <jason.swails.gmail.com> wrote:
On Wed, Feb 10, 2016 at 7:26 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>
wrote:
> Dear all
> I am trying to do energy minimization with my protein, unfortunately it
> was stopped and gave the following error:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 71 NaN NaN 0.0000E+00 N 1
> BOND = NaN ANGLE = NaN DIHED =
> NaN VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -48743.1044 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> 0.0000
>
>
The pd
>
> b file of protein as well as output file are attached.
> Your h
>
> elp in this regard would be appreciated.
>
This is weird. The first step has EGB becoming NaN with the igb=1 model.
A couple ideas -- try a short minimization in the gas phase (igb=6). Also
see if igb=2 or igb=5 gets the same kind of problems.
Also look in your prmtop file for the flag RADIUS_SET. What is the value
there?
HTH,
Jason
>
> All the bestMaryam
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 10 2016 - 05:30:04 PST
