On Sun, Apr 07, 2013, 涂志萍 wrote:
> I am calculating a protein with ab initio method using explicit water
> model.But when I minimize the solvent environment energy, I find that the
> term of VDWAALS in the min1.out file are very large, which made the
> protein disconected.
> BOND = 85.8983 ANGLE = 234.2699 DIHED = 1642.1355
> VDWAALS = 34036816.3028 EEL = 71478981.6109 HBOND =
> 0.0000
> 1-4 VDW = 284.0258 1-4 EEL = 3914.3180 RESTRAINT =
> 1.0803
> EAMBER = *************
This is probably a problem with your initial structure; use the checkoverlap
command in ptraj to see if two atoms are very nearly on top of one another.
Also, set ntpr to 1 and maxcyc to a small number like 20, in order to get more
detailed information about what is going on. If you find bad parts of the
structure, you will have to correct them.
Aside: nothing is gained by using a very large cutoff here: consider using the
default.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 07 2013 - 06:30:03 PDT
