Re: [AMBER] Dielectric constant for solute

From: Jason Swails <>
Date: Thu, 3 Feb 2011 09:59:46 -0500

If you add "-rewrite-output" to the command-line, it will skip all of the
calculations and just print the output files. However, you still have to
provide the input files and topology files (and all other files you provided
when you ran the calculation) so that knows what files to look

Good luck!

On Thu, Feb 3, 2011 at 9:31 AM, mish <> wrote:

> Hi all:
> I have few quarries and some problem on MM/PBSA and NMODE calculations :
> 1- If I use script with DIELC =1 and INTDIEL=2 in .Gb section:
> what I can see is that ELE for gas phage changes, where as I wanted to
> change the solute dielectric constant for solvation free energy
> calculation
> only. Is it reasonable to change DIELC =2 or 3 to get reasonable nimsing
> free energy with experiment ?
> 2- I was doing entropy calculation with python script and due to some
> reason
> my calculation were killed after 30 days. I have all the output data from
> calculated threads, Will it be possible, through python script, to generate
> the statistics from the previously calculated trajectories ? something like
> in perl version ?
> ..mish
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Feb 03 2011 - 07:30:07 PST
Custom Search