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Joined: Jun 2017
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Hi,
I understand it must be routine to perform these experiments, but due to my lack of much expertise in the field I have no other option but to ask here. I want to perform refolding kinetics of a protein (Go model) using gorex.pl module, but for that I need initial unfolded conformations. I can probably perform thermal heating at high temperature e.g. 500K to 550 K (go replica exchange limit) with 4 to 8 replicas to get good exchange. But I am not sure how to obtain different starting conformations. Probably different pdb's can be extracted after specific number of cycles. But how do I decide which ones to choose from. Or I will really appreciate if there is any other more recommended solution.

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These are all interesting questions, but at this stage not really CHARMM questions. CHARMM can probably do most of what you want - but you have to decide what you want. I suggest that you discuss with your supervisor, and then ask more specific questions here on how to implement any given strategy using CHARMM.


Lennart Nilsson
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I think someone associated with MMTSB (or an experienced user) used to answer some questions here, but it has been a year or more.

Have you tried the email link at www.mmtsb.org ?


Rick Venable
computational chemist

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@ Lennart. Thank you for the suggestions. Actually I work in a experimental protein folding lab. And there is some part where I am not able to reach experimentally i.e. to understand initial stage of refolding kinetics. And this is why I wanted to perform some computational studies. I haven't talked to my supervisor in details about it though but I have had some experience with theoretical chemistry and simulation studies in past and that's why I thought of these studies. There are some publications who discuss similar methodology using gorex.pl tool but not in much details.

@Rick. I think I should try to write to mmtsb.org also. May be that 'll work. Thanks for the suggestion.


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