AMBER Archive (2008)

Subject: AMBER: Tutorial B3- Section6

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed Apr 09 2008 - 20:30:27 CDT

Hi
I followed the tutorials B3 and try to reproduce the data.

After type the two commands,
$AMBERHOME/exe/ptraj TC5b.prmtop < measure_rmsd.trajin > measure_rmsd.out
$AMBERHOME/exe/ptraj TC5b.prmtop < extract_frame9_2455.trajin > extract_frame9_2455.out

I got the two following files and they are EMPTY.
extract_frame9_2455.out
measure_rmsd.out

$AMBERHOME/exe/ptraj TC5b.prmtop <mdcrd_to_binpos.ptraj >mdcrd_to_binpos.out
Also, I got a EMPTY mdcrd_to_binpos.out
and there are no equil_1-10.binpos files

any ideas for this?
by the way,
when I install Amber, patch #40 did not successful.
is this a crucial thing to make the above problems??

Thanks
Lin

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