AMBER Archive (2005)

Subject: Re: Re: AMBER: Protein with structural ions

From: Y. Xu (yxu_at_mail.sioc.ac.cn)
Date: Fri Apr 08 2005 - 01:39:45 CDT

Dear Tim Meyer

        

======= 2005-04-07 16:05:00 £º=======

>> In my simulational system, there are three HIS coordinated with Zn2+. several MD simulation were performed with different ligands (the initial conformation of Ligands is from the result of autodock).
>> I found that in one simulation three HIS residues keep a distance ~ 2A with Zn during 500 ps. But in some other trajectory, only two HIS keep this optimal coordinated distance, ~2A.
>
>have you thought to use deprotonated HIS?
those protonized state is cited from reference, I think it is correct.

>see
>
http://amber.scripps.edu/0Net/ions
>
>tim
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Best regards!
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Y. Xu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yxu_at_mail.sioc.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-04-08
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* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* yxuemail_at_sina.com
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¡¡¡¡¡¡¡¡¡¡¡¡

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