Hello.
Attached is my input file and output file for xplor for covariance
analysis.
I have got 7 dcd files with 800 frame for each dcd file each 500
fs steps and in total 400000 steps for each dcd file (400ps)
The output file reads only 800 (I think the last 800 ones).
1-
What is wrong with my input and can I add another dcd file with a
different time jump and less frames?
2-
Can I read several dcd files and go over all of them in one run?
Thanks, Dan.
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structure @3a4_1tqn.psf end
dynamics analysis covariance
asci=false
input=1.dcd
input=2.dcd
input=3.dcd
input=4.dcd
input=5.dcd
input=6.dcd
input=7.dcd
begin= 0 skip= 500 stop= 2800000
set1=(name ca)
set2=(name ca)
output=3a4_ca.matrix
end
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XPLOR-NIH version 2.13
C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger
N. Tjandra, and G.M. Clore
J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih
User: danfishl on: x86/Linux at: 9-Apr-06 10:06:33
X-PLOR>structure @3a4_1tqn.psf end
ASSFIL: file /data4/c/danfishl/cyp/correlations/3a4_1tqn.psf opened.
STRUcture>PSF
* 3A4 CPDI+ 16A SOLV
* DATE: 1/30/ 6 11:52: 6 CREATED BY USER: danfishl
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 70137(MAXA= 102400) NBOND= 70235(MAXB= 102400)
NTHETA= 35095(MAXT= 51200) NGRP= 23158(MAXGRP= 25600)
NPHI= 21005(MAXP= 25600) NIMPHI= 1254(MAXIMP= 1600)
NDON= 815(MAXPAD= 25600) NACC= 21494(MAXPAD= 25600)
NNB= 0(MAXNB= 100)
STRUcture>
STRUcture>
STRUcture> end
X-PLOR>
X-PLOR>
X-PLOR>dynamics analysis covariance
COVAR>
COVAR> asci=false
COVAR>
COVAR> input=1.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/1.dcd opened.
COVAR> input=2.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/2.dcd opened.
COVAR> input=3.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/3.dcd opened.
COVAR> input=4.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/4.dcd opened.
COVAR> input=5.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/5.dcd opened.
COVAR> input=6.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/6.dcd opened.
COVAR> input=7.dcd
ASSFIL: file /data4/c/danfishl/cyp/correlations/7.dcd opened.
COVAR>
COVAR> begin= 0 skip= 500 stop= 2800000
COVAR>
COVAR>
COVAR> set1=(name ca)
SELRPN: 472 atoms have been selected out of 70137
COVAR> set2=(name ca)
SELRPN: 472 atoms have been selected out of 70137
COVAR>
COVAR> output=3a4_ca.matrix
COVAR>
COVAR>end
ASSFIL: file /data4/c/danfishl/cyp/correlations/3a4_ca.matrix opened.
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/05/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:28: 3 CREATED BY USER: danfishl
READC: reading file= 1 ISTART= 500
READC: 70137 atoms were "free"
READC: BEGIN not compatible. Modified
READC: NUNIt= 7
READC: BEGIn= 500 SKIP= 500 STOP= 2800000
READC: TIMEstep= 0.00000000 ps header= CORD
READC: EOF on file= 1 while trying to read step= 400500
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/06/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:32:14 CREATED BY USER: danfishl
READC: reading file= 2 ISTART= 500
READC: 70137 atoms were "free"
READC: mismatch correction; file-number= 2
READC: EOF on file= 2 while trying to read step= 400500
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/07/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:35: 6 CREATED BY USER: danfishl
READC: reading file= 3 ISTART= 500
READC: 70137 atoms were "free"
READC: mismatch correction; file-number= 3
READC: EOF on file= 3 while trying to read step= 400500
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/08/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:37:22 CREATED BY USER: danfishl
READC: reading file= 4 ISTART= 500
READC: 70137 atoms were "free"
READC: mismatch correction; file-number= 4
READC: EOF on file= 4 while trying to read step= 400500
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/08/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:39:44 CREATED BY USER: danfishl
READC: reading file= 5 ISTART= 500
READC: 70137 atoms were "free"
READC: mismatch correction; file-number= 5
READC: EOF on file= 5 while trying to read step= 400500
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/09/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:42:39 CREATED BY USER: danfishl
READC: reading file= 6 ISTART= 500
READC: 70137 atoms were "free"
READC: mismatch correction; file-number= 6
READC: EOF on file= 6 while trying to read step= 400500
REMARKS FILENAME=nano_all.dcd CREATED BY NAMD
REMARKS DATE: 03/10/06 CREATED BY USER: danfishl
* DATE: 4/ 9/ 6 9:45:58 CREATED BY USER: danfishl
READC: reading file= 7 ISTART= 500
READC: 70137 atoms were "free"
READC: mismatch correction; file-number= 7
READC: EOF on file= 7 while trying to read step= 400500
%READC-EOF file 7 at step 400500
READC: complete. 800 coordinate sets were passed to calling routine
%NEXTF-ERR: EOF or ERROR encountered on input:
^^^^
HEAP: maximum use= 11519116 current use= 9162602
X-PLOR: total CPU time= 29.2300 s
X-PLOR: entry time at 10:06:33 9-Apr-06
X-PLOR: exit time at 10:08:28 9-Apr-06
