AMBER Archive (2000)

Subject: Re: Problems using IBELLY in AMBER6

From: Marios Philippopoulos (mphilip_at_sickkids.on.ca)
Date: Mon Feb 28 2000 - 17:24:22 CST

I was using BELLY in an effort to minimize and equilibrate the solvent
prior to
doing so on the full system. The problem is that ewald is turned on by
default
(in the input files I sent out I specified the box dimensions for ewald,
but I get
the same error message even without doing so), and I don't know how to
turn it off
prior to invoking BELLY.

Please see, for example, the following output:

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

  Minimization of solvent (solutes are fixed):
 &cntrl
   imin=1, maxcyc=200, scee=1.2, ntpr=20, ibelly=1,
 &end
Allow only solvent (residues 3 to 824) to move:
 RES 3 824
 END

...........................
...............

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

-----------------------------------------------------------------------------------

Thanks,

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