Re: [AMBER] loading molecule in leap

From: David A Case <>
Date: Wed, 27 May 2015 08:30:15 -0400

On Wed, May 27, 2015, jacob wick wrote:
> I want to study Lipoteichoic acid using AMBER.
> Please tell me how to prepare an amber compatible pdb file ( so that I can
> add partial charges to the molecule).
> I have drawn this big molecule using marvin sketch but now I am confused
> how to add partial charges to such a big system and how to load the
> molecule in leap.

Wow. This is like the old joke about buying a yacht: if you have to ask how
much it costs, you can't afford it.

After you work through the tutorials, start with the repeating units
(built up from derivatives of glycerol phosphate, then slowly add chemical
components. You are certainly going to want to treat this as a polymer,
not some large single molecule. Maybe other people on the list will have
ideas or know of some relevant studies. For some inspiration, take a look at
Section 3.8 (on lipids) in the Amber Reference Manual.


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Received on Wed May 27 2015 - 06:00:05 PDT
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