AMBER Archive (2004)

Subject: Re: AMBER: Sander went through

From: Rhonda Torres (torres_at_scripps.edu)
Date: Fri May 28 2004 - 19:49:44 CDT

Hi Bo,

In order to get some background on MD calculations, you might want to read
Leach's book:

"Molecular Modelling: Prinicples and Applications" by Andrew R. Leach

This should answer many of your general questions.

Hope this helps.

Rhonda

-----------------------------------
Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

email: torres_at_scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896

On Fri, 28 May 2004 bybaker_at_itsa.ucsf.edu wrote:

> 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_at_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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