Dear Sir:
I met a problem when I using AMBER6, accroding to the tutorial of
Streptavidin/biotin complex, partially solvated ( Build biotin, load
complex, partially solvate, equilibrate dynamics). I can not get the
result of min.out as the tutorial gives. The following is what I got:
-----------------------
-------------------------------------------------------
Amber 6 SANDER Scripps/UCSF 1999
-------------------------------------------------------
| Sun Mar 26 18:06:51 2000
[-O]verwriting output
File Assignments:
|MDIN :
min.in
|MDOUT:
min.out
|INPCR:
stbtcap.crd
|PARM :
stbtcap.top
|RESTR:
min.rst
|REFC :
refc
|MDVEL:
mdvel
|MDEN :
mden
|MDCRD:
mdcrd
|MDINF:
mdinfo
Here is the input file:
&cntrl
imin=1, maxcyc=100, ntpr=20, scee=1.2, nsnb=999999,
ntmin=2,
&end
-------------------------------------------------------------------------------
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:
| Using the SGI specific (ZFFT3D) Fast Fourier Transform
-------------------------------------------------
NO EWALD INPUT FOUND: USING DEFAULTS
-------------------------------------------------
Largest sphere to fit in unit cell has radius = 1.026
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: 0.10261E+01
Check ew_legal.h
-----------------------------
I am a newman to AMBER,hope you can give me some suggestion about my
problem. Thanks a lot.
Regards,
mao
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| Mao Xiang |
| Lab of Molecular Regulation for Microbial Secondary Metabolism |
| Shanghai institute of Plant Physiology, Academia Sinica |
| 300 Fenglin Road, Shanghai, China, 200032 |
| Tel: +86-21-64042090-4791 |
| Fax: +86-21-64042385 |
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Received on Sun Mar 26 2000 - 02:18:00 PST
