AMBER Archive (2004)

Subject: Re: AMBER: Molecular dynamic & Acknowledgement

From: bybaker_at_itsa.ucsf.edu
Date: Tue Jul 13 2004 - 13:20:50 CDT

('binary' encoding is not supported, stored as-is) Hello, Ross:

Thank you very much for your scientific inputs on my question about MD.
Especially to provide me detailed suggestions about parameter setting.
>From your advice, I have a better understanding about conditions used for
molecular dynamic. I will give another run for the entire system, and
see how is going.

Best regards

Bo Yang

Hello, Andy and Josehp:

Thanks both of you forwarding the information of MSE!

I checked the crystallization paper, TAR is part of the buffer used for
the protein crystallization. In the crystal structure, one TAR molecule
is located near the region that is the major area turned to be unfolded
after MD. I may run the MD with or without TAR presence and see if there
is any effect from TAR.

All the best

Bo Yang

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