AMBER Archive (2008)

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

From: Thomas Leonard (thomasj_at_bii.a-star.edu.sg)
Date: Thu May 29 2008 - 07:01:43 CDT

Hi,

Thanks for your reply,
But even during the minimization (before MD) itself unusual bond formation
occurs in those specific nitogen carbon and oxygen.

Thomas

> 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
>
> --
> -------------------------------------------------------------------------------
> 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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