AMBER Archive (2006)

Subject: AMBER: problems with ptraj

From: anna.schrey_at_gmx.de
Date: Thu Aug 03 2006 - 09:49:39 CDT

dear amber specialists,

since Im obout to do a 100 ns simulation (pmemd, Amber8), I have to cut my tajectory for analysis. I tried this via ptraj:

ptraj sh3_cryst_water_ions.top sh3_cryst_long_cut.ptraj

with sh3_cryst_long_cut.ptraj:

trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd
trajout ./sh3_cryst_long_1_1000.mdcrd
go

The output was the following:

[...]
Successfully completed readParm.

PTRAJ: Processing input file...
       Input is from file sh3_cryst_long_cut.ptraj

PTRAJ: trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd
Checking coordinates: ./sh3_cryst_NTV_100200ps_orest.mdcrd

Could not open file (./sh3_cryst_NTV_100200ps_orest.mdcrd) with mode (r)
WARNING in checkCoordinates(): Could not open file (./sh3_cryst_NTV_100200ps_orest.mdcrd)
WARNING in ptrajSetupIO(): trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd, cannot open file...

PTRAJ: trajout ./sh3_cryst_long_1_1000.mdcrd
WARNING in ptraj(): No input trajectories specified (trajin), aborting...

I tested AMBER7 as well as AMBER8 ptraj and checked several times whether the input file exists. What might be the reason? Are there problems with detecting a pmemd trajectory file, or is something wrong with the extension to hinder autodetection?

regards,

Anna 

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