AMBER Archive (2006)

Subject: AMBER: "average" command in ptraj

From: Arjen-Joachim Jakobi (arjen.jakobi_at_web.de)
Date: Mon Apr 10 2006 - 07:15:16 CDT

I have a problem with the average command in ptraj. I would like to get the average structure for a number of specified frame intervals in a given trajectory. This is no problem if you read in the trajectory and dump the average for a single of these frame intervals. But, as I donīt like to generate input files for all these frame intervals (in my case every 50 ps) and read in the trajectory again and again, I would like to dump the averages by reading in the trajectory once and than drop the average structures by use of the [start] [stop] flags (see input below). However, this turned out to be impossible - ptraj generates a single average over the complete trajectory...

ptraj8.0 ../../min_XYZ.top << EOF

trajin ../../md10_XYZ.trj.gz

#strip :WAT

reference ../min_XYZ.pdb

rms reference out av_4000to4500ps.txt @CA

average av_4000to4050ps.pdb 1 50 pdb
average av_4050to4100ps.pdb 51 100 pdb
average av_4100to4150ps.pdb 101 150 pdb
average av_4150to4200ps.pdb 151 200 pdb
average av_4200to4250ps.pdb 201 250 pdb
average av_4250to4300ps.pdb 251 300 pdb
average av_4300to4350ps.pdb 301 350 pdb
average av_4350to4400ps.pdb 351 400 pdb
average av_4400to4450ps.pdb 401 450 pdb
average av_4450to4500ps.pdb 451 500 pdb
go

Can anybody help me to solve this issue? Thanks in advance!

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