Re: [AMBER] error with NMA calculation

From: David A Case <>
Date: Thu, 19 Nov 2015 08:12:46 -0500

On Wed, Nov 18, 2015, Mohammad Salem wrote:
> The system is 226 amino acids in a cage of solvent. For doing it
> “by hand”, can you give me suggestions for where the procedure is
> explained?

This is very will need a machine with a lot of memory and lots of

Also, using normal mode theory in a "cage of solvent" is very tricky and
non-standard thing to do. Unless you are very familiar with things like
"instanteous normal modes", you are likely to get results that you cannot

If you are new to normal modes, you should certainly gain some experience with
smaller systems before trying a system this large.


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Received on Thu Nov 19 2015 - 05:30:03 PST
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