rmsf calculation

Posted by: abir

rmsf calculation - 05/22/18 10:49 AM

I am new to charmm. I want to calculate rmsf using this following charmm script which is available in script archive.


* THIS SCRIPT IS FOR RMSF CALCULATION
*

stream toppar.str
! Read PSF
open read unit 10 card name step3_pbcsetup.xplor.ext.psf
read psf unit 10 card xplo

dele atom sele all .and .not (segid PROA .or. segid PROB) end
!dele atom sele all .and .not segid PROA end

! Read COOR
open read unit 10 card name step3_pbcsetup-nowater.crd
read coor unit 10 card

open read unit 51 file name output-protein.dcd

!traj firstu 52 nunit 1 begin 100 skip 100 stop 30000

coor dyna firstu 51 nunit 1 begin 100 skip 100 end 30000
orient select(segid PROA .or. segid PROB) end
!delete atom sele .not. segid main end ! we don't want rmsd for the waters
set R1 1 ! this fragment starts with residue 1
open unit 21 write form name rmsf.dat
stream rmsf-residue.str

stop


But I get this error message:

CHARMM> coor dyna firstu 51 nunit 1 begin 100 skip 100 end 30000

***** LEVEL 0 WARNING FROM *****
***** SELEction keyword missing
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


please help in this regard.
Posted by: rmv

Re: rmsf calculation - 05/22/18 11:45 AM

The trailing dash (-), which indicates a continued command, appears to be missing from the end of the COOR DYNA line; the line following is part of that command, but is read incorrectly due to the missing dash. Please read usage.doc and pay more attention to command syntax.
Posted by: abir

Re: rmsf calculation - 05/23/18 09:48 AM

Thanks Rick, I get the rmsf value.