I have few dcds which i want to merge and recenter.
Code:
READ PSF CARD NAME ./../eqf10/@EQHEATPSF
READ COOR PDB NAME ./../eqf10/@EQHEATPDB
open read unit 51 file name ../output/@i/unfold_1le0.job0.@i.sort.dcd
open read unit 52 file name ../output/@i/unfold_1le0.job1.@i.sort.dcd
!!!!!TRAJECTORY FIRSTU 51 NUNIT 1 IREAD BEGIN 0 STOP 10000000 SKIP 2500
!!!!!TRAJ READ
open write unit 61 file name ./../anal/recen/@i/unfold_1le0.joball.@i.recen.dcd
! Here you need the same set of image or crystal definitions as were used
! when the trajectory was created
crystal define CUBIc 50. 50. 50. 90.0 90.0 90.0
crystal build noper 0
! Image statemnts for those molecules that should be recentered
image byresidue sele all end
merge firstu 51 nunit 2 skip 0 output 61 - !!!!begin 0 stop 10000000 -
orient recenter sele all end sele segid PRT .and. .not. hydrogen end
this script runs fine for single dcd. i want to run it on 2 or more dcd's. but this only writes first dcd to unit 61. how can i merge these dcd's.
Try using the NFILE option of the MERGE command, and set it to the sum of the number of frames from all files. CHARMM expects to be merging consecutive dynamics files, and can have problems if the trajectory headers are not consistent with consecutive files.
You can get some clues from TRAJ QUERY, after the files are OPENed:
Tried few modification but still it writes only 1 dcd to all.dcd
Code:
open read unit 51 file name ../output/@i/unfold_1le0.job0.@i.sort.dcd
open read unit 52 file name ../output/@i/unfold_1le0.job1.@i.sort.dcd
TRAJ QUERY UNIT 51
TRAJ QUERY UNIT 52
calc ntot = 2 * ?nfile
TRAJECTORY FIRSTU 51 NUNIT 2 IREAD BEGIN 0 SKIP 1
!!!!!TRAJ READ
!!!!!!!!!!open unit 61 write file name @odcd
open write unit 61 file name ./../anal/recen/@i/unfold_1le0.joball.@i.recen.dcd
! Here you need the same set of image or crystal definitions as were used
! when the trajectory was created
crystal define CUBIc 50. 50. 50. 90.0 90.0 90.0
crystal build noper 0
! Image statemnts for those molecules that should be recentered
image byresidue sele all end
merge firstu 51 nunit 2 skip 1 output 61 nfile @NTOT begin 0 stop 8000 -
orient recenter sele all end sele segid PRT .and. .not. hydrogen end
!================================================================
! Crystal definition and cutoffs
!================================================================
set ci 10. ! inner switching cutoff
set rc 12. ! cutoff
set ctl 14. ! list-cutoff
set xo 14. ! cutoff for crystal
set 6 50.
set ang 90
crystal defi cubic @6 @6 @6 @ang @ang @ang
crystal build Noper 0
IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE ALL END
IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE RESNAME TIP3 END
!================================================================
!Set up for reading coordinate sets from trajectory and writing data
!================================================================
OPEN UNIT 51 READ UNFORMATTED NAME ../output/@i/unfold_1le0.job0.@i.sort.dcd
OPEN UNIT 52 READ UNFORMATTED NAME ../output/@i/unfold_1le0.job1.@i.sort.dcd
OPEN WRITE UNIT 19 FILE NAME ./../anal/recen/@i/unfold_1le0.joball.@i.recen.dcd
TRAJECTORY QUERY UNIT 51
CALC NTOT = ?NFILE * 2
TRAJECTORY NUNIT 2 IREAD 51 IWRITE 19 SKIP 1 NFILE @NTOT
!================================================================
!Loop for reading coordinate sets and calculating distances
!================================================================
SET i 1 ! loop index i
LABEL LOOP
TRAJECTORY READ
UPDATE
TRAJECTORY WRITE
INCREMENT i
IF i LE @NTOT GOTO LOOP
STOP
Even this gives error as follows
Code:
CHARMM> TRAJECTORY WRITE
TRAJ: WRITING NEXT TRAJECTORY FILE, OPTIONS;
SKIP= 1 NPRIV= 0 NSTEP= 8000 TRAJU= 19
CHARMM>
CHARMM> INCREMENT i
Parameter: I <- "2"
CHARMM> IF i LE @NTOT GOTO LOOP
Parameter: NTOT -> "8000"
Comparing "2" and "8000".
IF test evaluated as true. Performing command
CHARMM>
CHARMM> TRAJECTORY READ
***** LEVEL -1 WARNING FROM <REATRJ> *****
***** INPUT TRAJECTORY NOT SET UP.
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5
Check for other messages, esp. from opening the input trajectory files.
If the files were not produced by CHARMM or have been modified by some other program, the file headers may not conform to what is expected by CHARMM, which can cause problems such as this.
I have checked the above script with TRAJ and MERGE command. This works fine for DCD from Charmm but it gives error with DCD coming from NAMD.
I have Also noticed that while reading Charmm gets some extra information like number of previous steps while reading charmm dcd but this is set to 0 if dcd is read from namd.
