Dear AMBERers,
I am now trying to perform a typical molecular dynamical simulation on a
protein/ligand system with AMBER 6: First, I cover the binding site with a
water cap, and define a subset which contains the ligand and the adjacent
residues/waters. Then the subset is minimized while the rest part of the
whole system keeps frozen. Then I would like to perform a MD on the subset
(the so-called Belly run).
I used the following input file for the MD simulation:
--------------------------------------------------------------
cold start belly equil
&cntrl
ibelly=1, imin=0, irest=0, ntx=1,
tempi=0.0, tautp=2.0, temp0=298.0, ntt=1, dtemp=5.0,
ntb=0, ntp=0,
ntc=2, ntf=2,
nstlim=10000, dt=0.002,
igb=0, scee=1.2, cut=12.0,
ntwe=25, ntwx=25, ntpr=25,
&end
-- belly = residues 14A from HAP
RES ...
RES ...
END
END
-------------------------------------------------------------
But the program would not run and it told me this:
-----------------------------------------------------------------------
...
1. RESOURCE USE:
EWALD SPECIFIC INPUT:
| Using the SGI specific (ZFFT3D) Fast Fourier Transform
-------------------------------------------------
NO EWALD INPUT FOUND: USING DEFAULTS
-------------------------------------------------
Largest sphere to fit in unit cell has radius = 0.000
Ewald PARAMETER RANGE CHECKING:
parameter skinnb+cutoffnb: (nonbond list cut) has value 0.13000E+02
This is outside the legal range
Lower limit: 0.00000E+00 Upper limit: 0.00000E+00
Check ew_legal.h
-----------------------------------------------------------------------
So, what is this supposed to mean? I will appreciate it if anybody can
figure out the problem.
Best wishes,
Renxiao Wang
renxiao_at_chem.ucla.edu
Received on Tue May 30 2000 - 16:46:03 PDT
