Re:

From: ˴ (zhongshun0643_at_gmail.com)
Date: Fri Jul 20 2012 - 02:38:00 CDT

****Dear

   Firstly, thank you for the answer!

   What I want to do is to simulate the interaction between a protease and
a polypeptide chain by NAMD.It is known that the active sites of the
protease can interact with certain amino acid of the polypeptide. In my
opinion they can react with each other and reach suitable conformations
which are good for endonuclease reaction after enough steps of NAMD run.
And the free energy of the interaction can also be calculated.
   And I am wondering if this simulation is similiar with the dock of
protein and small molecular.
   I don't know how to do it in details for there seems no related
tutorials online.I just tried to segment the proteins and pepsin into one
pdb file, only to find they are too far away from each other.Then I don't
know what to do next and hope you can help me.
   By the way, could you offer me some other tutorial.

Best regards,

shun zhong

2012/7/17 Norman Geist <norman.geist_at_uni-greifswald.de>

> Hi,****
>
> ** **
>
> Of course you can simulate such things. But keep in mind that this is
> classical molecular dynamics so theres no possibility to simulate bond
> breaking and creating. You will see the electrostatic and vdw interaction
> between the proteins.****
>
> ** **
>
> Do give you more detail, we will first need more detail on what you want
> to do. Especially what nature the reaction/interaction is.****
>
> ** **
>
> Norman****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *??
> *Gesendet:* Montag, 16. Juli 2012 15:59
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: ****
>
> ** **
>
> Dear all,
> ****
>
> I have learnt NAMD tutorial on your Web. And now I am wondering
> if I can use NAMD to simulate a system containing two or more protein, then
> obtain the interaction or reaction between these proteins. If can, could
> you tell me how to do it in details?****
>
> ****
>
> ****
>
> Thanks in advance!
> Best regards, ****
>
> shunzhong****
>
> --
> ----------------------------------------------------------------------------------------
> ****
>
> shun zhong****
>
> Graduate Student of Technical Institute of Physcis and Chemistry, CAS****
>
> Beijing, P.R.China, 100190****
>
> Web: htthttp://www.ipc.ac.cn/****
>

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