AMBER Archive (2007)

Subject: Re: AMBER: New 2 the board

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 12 2007 - 18:03:46 CST

On Wed, Dec 12, 2007, Campbell, Patrick wrote:
>
> I am a student and I have recently started the usage of AMBER for protein
> optimization. The question that I have might have a straightforward response
> so do bear with me.
>
> I have created an input file (run.com) for the optimization of my protein.
>
> My PDB protein is saved in my working directory under the name LTR. I have
> also saved the input file (shown above) under the name run.com - I thus have
> two files in my working directory.
>
> I would like to optimize the PDB file and would like to know how the link
> between the input file and the PDB file is made.

Sounds like you need to start with the tutorials; there are intermediate
steps to take between having a pdb file and running sander.

http://amber.scripps.edu/tutorials

...dac

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