AMBER Archive (2000)

Subject: problem in AMBER

From: Mao Xiang (xmao_at_iris.sipp.ac.cn)
Date: Sun Mar 26 2000 - 04:18:00 CST

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 |
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~