Hello, Amber:
Thanks for the help on running Sander. I really appreciate all the responses.
I have fixed the input file format, and set ‘ntb=0’. This time, sander
went through!!
As you can see, I am a new user of Amber. This program provides a
reasonable way to do molecular dynamic and is much more flexible for user
to define the conditions. It may be hard for beginner to understand how
the parameters are set. Can I ask some general questions? First, in which
condition a ‘periodic box’ needs to be set for energy minimization run?
And what is the definition of ‘free energy’? I have looked at the AMBER
manual and some of the references, but still could not get clear on it.
Thank you!
Best regards
Bo Yang
On Thu, 27 May 2004 16:15:37 -0700 "David A. Case" wrote:
> On Thu, May 27, 2004, bybaker.itsa.ucsf.edu wrote:
> >
> > I don't know why sander could not find cntr1 namelist. Please help.
>
> The namelist name is "cntrl" (last letter is "ell"), short for "control"
>
> You are typing in "cntr1" (last digit is the number "1"):
>
> > &cntr1
>
> ...dac
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Received on Sat May 29 2004 - 01:53:00 PDT
