AMBER Archive (2000)

Subject: Problems using IBELLY in AMBER6

From: Marios Philippopoulos (mphilip_at_sickkids.on.ca)
Date: Mon Feb 28 2000 - 13:53:51 CST


Hello everyone,

I have run into problems when trying to use IBELLY in a minimization
run. Here is
my input file. I am minimizing two solute molecules in a box of TIP3
waters:

---------------INSERT--------------------------------------------------

Steepest-Descents minimization of the solvent (solutes are kept fixed):
 &cntrl
   imin=1, maxcyc=200, scee=1.2, ntpr=20, ibelly=1,
   ntwx=20, ntmin=2,
 &end
 &ewald
   a=30.538, b=30.538, c=30.538,
 &end
Allow only solvent (residues 3 to 824) to move:
 RES 3 824
 END
END

--------------END---INSERT---------------------------------------------

In the output file I get the following messages (end of file shown):

----------------INSERT-------------------------------------------------
...
......
.............
Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!

    LOADING THE BELLY ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 Allow only solvent (residues 3 to 824) to move:
 GRP 1 RES 3 TO 824
      Number of atoms in this group = 2466
    ----- READING GROUP 2; TITLE:
 END

     rfree: End of file on unit 5

--------------END--INSERT-----------------------------------------------

Thank you for any advice.

Sincerely,

Marios Philippopoulos

--
Marios Philippopoulos, PhD
Structural Biology and Biochemistry Programme
Hospital for Sick Children
555 University Avenue
Toronto Ontario Canada M5G 1X8

mphilip_at_sickkids.on.ca