I ran the script using psf, pdb, and traj made from your merge script and deleted water.
The error I get running the rmsd-rgyr script is:
At line 959 of file dynio.f
Fortran runtime error: End of file
The output file is attached.
This is the input file:
!*FILENAME: rmsd-rgyr.inp
!*PURPOSE: compute rmsd vs initial structure and radius of gyration from
!trajectory
!*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
!*
!unix environment variable CHM_HOME points to CHARMM installation
!directory
stream toppar.str
read psf card name "new_psf.psf"
open unit 2 card read name -
"test.pdb"
read coor pdb resid unit 2
! put reference coordinates into comparison set as well
coor copy comp
open unit 11 write form name rmsd.dat
write title unit 11
* time rmsd
*
open unit 12 write form name rgyr.dat
write title unit 12
* time rgyr
*
! assume this is a trajectory where overall translation/rotation has been
!removed and
! without water or other unnecessary things
open unit 51 read unform name -
"traj_all.cor"
correl maxtime 10000000
enter v1 rms
enter v2 gyra
traj firstu 51
write v1 dumb time unit 11
*hi
*
write v2 dumb time unit 12
*hi
*
end
