AMBER Archive (2008)

Subject: Re: AMBER: how to overcome theunusual bonds formation

From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Thu May 29 2008 - 06:54:20 CDT

Hi,

On Thursday, 29. May 2008 13:03, Thomas Leonard wrote:
> Hi,
>
> Why unusual bonds are formed during minimization.
>
> In my case I have problem with unusual bond formation (which is not
> expected) at the nitrogen,oxygen of FADH cofactor

in normal MD simulation no bond breaking can occur.

Your question is not clear to me, I think you have done following:

If you calculate an average structure of your simulation and than view it as a
pdb file, than you can see "unphysical bonds".
Easy solution is to minimize this average structure.

>
> Thomas
>
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Greetings,

Florian 

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
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 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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