AMBER Archive (2007)

Subject: AMBER: problem with ptraj with calculating auto time correlation functions

From: Terry Lang (terry_at_lego.berkeley.edu)
Date: Fri Mar 09 2007 - 12:36:14 CST

Dear AMBER Community,

       I am trying to calculate some auto and cross time correlation
functions but have run into a snag. I am trying to use the following
script to compute both auto and cross time correlations:

#!/bin/csh

ptraj prot.prm << EOF
trajin full_md_pres.crd
trajin run.crd
trajin run2.crd
trajin run3.crd
reference prot.crd
strip :WAT
strip @H
strip @Na+
rms reference
vector a1 :187 corr :233
vector a2 :188 corr :232
analyze timecorr vec1 a1 out a1.out
analyze timecorr vec1 a2 out a2.out
analyze timecorr vec1 a1 vec2 a2 out a1_a2.out
EOF

However, the only output I am getting is the a1_a2.out file. What am I
doing wrong?

Thanks,
Terry 

-- 
P. Therese Lang
Post Doc
Alber Lab, UC Berkeley

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