Re: AMBER: New 2 the board

From: David A. Case <>
Date: Wed, 12 Dec 2007 16:03:46 -0800

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 ( 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 - 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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 16 2007 - 06:07:11 PST
Custom Search