Re: [AMBER] Targeted MD shows blank output file!

From: Carlos Simmerling <>
Date: Wed, 4 Mar 2015 08:37:23 -0500

you might also give thought to starting from low rmsd and then moving
toward high.... les likely to get stuck that way. either way, you'll have
to spend time thinking about what the results really mean. I would not
interpret them as giving you a folding "path". Look in the literature too,
there is a long history of forcing things to fold/unfold and analyzing the
results (though not as much recently, these approaches have fallen out of

On Wed, Mar 4, 2015 at 8:12 AM, Jason Swails <> wrote:

> > On Mar 4, 2015, at 8:05 AM, Pallavi Mohanty <>
> wrote:
> >
> > Thanks Carlos and Jason for your prompt relies!
> > Do you mean to say that i need to change below mentioned part marked in
> red
> > to get the desired output?
> You are asking targeted MD to make an *enormous* change. I have no idea
> how long it will take to fold a structure like this. I would suggest
> looking at previous studies to see what has worked in the past, and then
> appropriately scale it up to your problem. Even then, there is no
> guarantee it will work.
> Also, nothing showed up as ‘red’ in my email client. Not all email
> clients respect HTML markup (and some display it horribly). I would
> suggest using some other approach to indicate where you changed values.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Mar 04 2015 - 06:00:03 PST
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