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rmsf calculation
#36974 05/22/18 02:49 PM
Joined: Apr 2018
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abir Offline OP
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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.

Re: rmsf calculation
abir #36975 05/22/18 03:45 PM
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Posts: 8,470
rmv Online Content
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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.


Rick Venable
computational chemist

Re: rmsf calculation
abir #36980 05/23/18 01:48 PM
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abir Offline OP
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Thanks Rick, I get the rmsf value.


Moderated by  lennart, rmv 

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