Hi Lennart,
To be honest, my original .pdb, .psf and .crd files were transfored from Amber program. Then, I perfomed the below script to modify the format of these three files. This is my input script, I deleted 78342 atoms :
----------------------
* charmm input file for smll testsystem
*
bomblevel -1
wrnlev 5
prnlev 6
set jobname 19.9
set outjob mcp
set inputdir ./input
set topname ./toppar/parm14sb_all.rtf
set parname ./toppar/parm14sb_all.prm
! Topology files standard one
open read unit 1 card name @topname
read rtf card unit 1
close unit 1
! Parameter files
open read unit 2 card name @parname
read para card unit 2
close unit 2
!stream @{strname}
! psf file
open read unit 2 card name @{inputdir}/@{jobname}.psf
read psf card unit 2
close unit 2
open read form unit 13 name @{inputdir}/@{jobname}.crd
read coord card unit 13
close unit 13
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
set safesphere 49
delete atom sort select .byres. -
( .not.( point 46. 57. 92. cut @safesphere ) -
.and. ( segid SYS .or. segid SSS) ) -
end
!delete atom sort select segid SSS end
!
JOIN SYS renu
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
IOFOrmat NOEXtended
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
open write card name ./@{outjob}.crd unit 41
write coordinates card select all end unit 41
* Coordinates after simulation of all atoms in protein,
* noextend crd format
*
open write card name ./@{outjob}.psf unit 49
write psf card unit 49
* This is the PSF for the structure of protein,
* noextend format
*
! Punch out the PDB
open write unit 19 card name ./@{outjob}.pdb
write coor pdb unit 19
* This is the PDB for the structure of PROTEIN
*
close unit 19
stop
---------------------------
Thank you for helping me!
