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

From: nicholus bhattacharjee <nicholusbhattacharjee.gmail.com>
Date: Fri, 30 Oct 2009 06:18:45 -0400

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
>quit

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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 30 2009 - 03:30:02 PDT
Custom Search