AMBER Archive (2009)

Subject: [AMBER] Is it the way to do simulation in vacuum

From: nicholus bhattacharjee (
Date: Fri Oct 30 2009 - 05:18:45 CDT

Dear community,
                          I am trying to simulate my protein in vacuum. I am
preparing the topology and parameter files as follows

$ tleap
> source leaprc.ff99SB
> mol=loadpdb pdb
> saveamberparm mol prmtop inpcrd

Then I have run the minimization of 250 cycles. But this small minimization
is not coming out. And investigating the output file by "tail -f" command
only shows the following
   AMBER 9 SANDER 2006

I am unable to find the defect in the procedure. Please help.

Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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