I m not sure if this script is understood. Right before the small script component below, we have a ready protein in waterbox with multiple water segid e.g. WAT2, WAT5, etc.

BOX was set to 70.But when i run the component below, we have a final octahedral of about 18A. Parameter A was founded also to have a value of 18A. Most of my protein residues are and water molecules are lost.

Can someone enlighten me?

set A @BOX ! parameters required for setup-truncated-octahedron.str
stream $CHM_STREAM/setup-truncated-octahedron.str
calc ax = @A * sqrt (0.75) ! required for crystal facilities
set b 109.4712206344907 ! same
coor conv align symm @ax @ax @ax @b @b @b

! save coordinates and psf
! C write psf card name @FILE-solv.psf
! * @FILE with crystal waters solvated with TIP3 waters, setup from top_all22_prot
! *
! write coor card name @FILE-solv.crd
! * @FILE with crystal waters solvated with TIP3
! * in rectangular box: @XSIZ x @YSIZ x @ZSIZ
! *

! save the PSF and coordinates for later use
open write formatted unit 27 name @FILE-solv.psf
write psf card unit 27
* with crystal waters solvated with TIP3 waters, par lipid-prot 27
*


open unit 1 write card name @FILE-solv.pdb
write coor pdb unit 1
* @FILE for viewing
* in rectangular box: @XSIZ x @YSIZ x @ZSIZ
*


! save size to file so we can reuse it
write title name @FILE-box-size.str
** PBC box definition for @FILE simulation
**
*set XSIZ @XSIZ
*set YSIZ @YSIZ
*set ZSIZ @ZSIZ
*set A @A
*return
*


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