AMBER Archive (2000)

Subject: What does this mean?

From: Renxiao Wang (renxiao_at_chem.ucla.edu)
Date: Tue May 30 2000 - 18:46:03 CDT


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