AMBER Archive (2009)

Subject: [AMBER] Issue related to vector saving

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Fri May 15 2009 - 08:35:01 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 :1-285_at_CA

vector v0 @547 corr @1699 out 142-236-48.vec order 2

vector v1 @547,@1699,@2839 corrplane order 2
analyze timecorr vec1 v1 vec2 v1 tstep 1 tcorr 10 out 142-236-48.tcorr
--------------------------------------------------------------------------------------------------------------------------------
the following out put i received from ptraj

PTRAJ: rms first mass :1-285_at_CA
Mask [:1-285_at_CA] represents 279 atoms

PTRAJ: vector v0 @547 corr @1699 out 142-236-48.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
142-236-48.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: :295-20533
  2> RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 1.00)
      Atom selection follows :2-94_at_CA,:97-189_at_CA,:192-284_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 cross-correlation 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 142-236-48.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
CSIR-SRF
Chemical Laboratory
Central Leather Research Institute
Adyar, Chennai, India- 600 020
       &
DAAD Research Scholar
EML-Research,Villa Bosch,
Schloss-Wolfsbrunnenweg 33
D-69118 Heidelberg
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