AMBER Archive (2009)Subject: [AMBER] Issue related to saving the vector in ptraj
From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Sat May 16 2009  07:41:10 CDT
Dear Amber users,
I would like to compute a vector using ptraj and i would like to save the
vector as the file.
I used the following input for ptraj but it does not produces the output
file. Please help me in this issue.
the following are the input file information
ptraj.in
trajin dyn.nc 1 10
strip :WAT
rms first mass :1285_at_CA
vector v0 @547 corr @1699 out 14223648.vec order 2
vector v1 @547,@1699,@2839 corrplane order 2
analyze timecorr vec1 v1 vec2 v1 tstep 1 tcorr 10 out 14223648.tcorr

the following out put i received from ptraj
PTRAJ: rms first mass :1285_at_CA
Mask [:1285_at_CA] represents 279 atoms
PTRAJ: vector v0 @547 corr @1699 out 14223648.vec order 2
Mask [@547] represents 1 atoms
Mask [@1699] represents 1 atoms
PTRAJ: vector v1 @547,@1699,@2839 corrplane order 2
Mask [@547,@1699,@2839] represents 3 atoms
PTRAJ: analyze timecorr vec1 v1 vec2 v1 tstep 1 tcorr 10 out
14223648.tcorr
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 10 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (/dyn.nc) is a NetCDF AMBER trajectory with box info with 10 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> STRIP: 60717 atoms will be removed from trajectory: :29520533
2> RMS to first frame using mass weighting
Dumping RMSd vs. time (with time interval 1.00)
Atom selection follows :294_at_CA,:97189_at_CA,:192284_at_CA
3> VECTOR: storage to array named v0
Calculate the vector between the center of mass of the two atom
selections
which follow (with the origin at the center of mass of the first)
Atom selection 1 is :48_at_CA
Atom selection 2 is :142_at_CA
The order of Legendre polynomials is 2
Warning: Output of corr, ired, corrired or corrplane vectors is not
yet supported!
4> VECTOR: storage to array named v1
Calculate the vector perpendicular to the least squares best plane
through the atom selection which follows
Atom selection is :48_at_CA,:142_at_CA,:236_at_CA
The order of Legendre polynomials is 2
ANALYZE
1> ANALYZE TIMECORR: Calculating crosscorrelation function of vector(s)
v1 v1,
for a correlation time of 10.000000, using a time step of 1.000000.
Corr. func. are not normalized
Corr. func. are calculated using the FFT approach
Results are written to 14223648.tcorr
Set 1 ..........
PTRAJ: Successfully read in 10 sets and processed 10 sets.
Dumping accumulated results (if any)
PTRAJ RMS: dumping RMSd vs time data
PTRAJ: Analyzing accumulated data
_______________________________________________________________________________________________________________
with regards
sundar

S.Sundar Raman
CSIRSRF
Chemical Laboratory
Central Leather Research Institute
Adyar, Chennai, India 600 020
&
DAAD Research Scholar
EMLResearch,Villa Bosch,
SchlossWolfsbrunnenweg 33
D69118 Heidelberg
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