Dear all,
I tried to follow the tutorial of biotin to do MD simulation with cap
water, but I got the following message when run minimization.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-------------------------------------------------------
Amber 6 SANDER Scripps/UCSF 1999
-------------------------------------------------------
| Run on Tue Apr 30 11:45:49 2002
[-O]verwriting output
File Assignments:
|MDIN : min_cap.in
|MDOUT: min_cap.out
|INPCR: fg_cap.crd
|PARM : fg_cap.top
|RESTR: min_cap.xyz
|REFC : fg_cap.crd
|MDVEL: mdvel
|MDEN : mden
|MDCRD: mdcrd
|MDINF: mdinfo
Here is the input file:
&cntrl
imin=1, maxcyc=1000, ntpr=20, scee=1.2, nsnb=999999, ntmin=2,
&end
-------------------------------------------------------------------------------
&cntrl
1. RESOURCE USE:
getting box info from bottom of parm
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info not found in inpcrd
EWALD SPECIFIC INPUT:
-------------------------------------------------
NO EWALD INPUT FOUND: USING DEFAULTS
-------------------------------------------------
Largest sphere to fit in unit cell has radius = 2.898
Ewald PARAMETER RANGE CHECKING:
parameter skinnb+cutoffnb: (nonbond list cut) has value 0.90000E+01
This is outside the legal range
Lower limit: 0.00000E+00 Upper limit: 0.28983E+01
Check ew_legal.h
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
So, I need to change the parameters in ew_legal.h file and recompile
sander?
Another question is what is the exact meaning for each term in file
ew_legal.h, and are there some recommandation values for thoes items?
Many thanks.
Xiaojian
Received on Tue Apr 30 2002 - 17:12:01 PDT
