From: Norman Geist (
Date: Fri Jul 20 2012 - 07:47:21 CDT



what you want to do is of course possible. A colleage of mine just simulated
the PLE with different substrates and mutations.


You can use VMD for example to adjust the molecules to each other if you
have copied the pdbs together (for example in VMD Mouse->Move->Fragment,
than just drag and drop the molecules)


Also you should get familiar with the pdb file format, where you could also
manipulate the coordinates itself by writing own scripts.


Norman Geist.


Von: [] Im Auftrag
von ??
Gesendet: Freitag, 20. Juli 2012 09:38
Betreff: Re: namd-l:




   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 <>



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.




Von: [] Im Auftrag
von ??
Gesendet: Montag, 16. Juli 2012 15:59
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,


shun zhong
Graduate Student of Technical Institute of Physcis and Chemistry, CAS
Beijing, P.R.China, 100190
Web: htt

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