AMBER Archive (2008)

Subject: RE: AMBER: stripping water from a restart file

From: CHAMI F. (fatima.chami_at_durham.ac.uk)
Date: Thu Oct 23 2008 - 06:33:29 CDT

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Bill Ross
Sent: Wed 22/10/2008 21:38
To: amber_at_scripps.edu
Subject: RE: AMBER: stripping water from a restart file
 
> What error msg was given?
>
> Unit 30 Error on OPEN: dimer-vac_md.rst_1000000=20

That unit number looks fishy. What args did you run sander with?

$AMBERHOME/exe/sander.MPI -O -i mdin -p dimer.prmtop -c dimer-vac_md.rst_1000000 -r jar_1.rst -o jar_1.out -x jar_1.mdcrd

I suspect that the topology file generated after stripping water using rdparm is different form the topology file generated by Leap

fatima

Bill
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