AMBER Archive (2008)

Subject: AMBER: Tutorial B3- Section6

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

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.

$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??


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to