CHARMM Development Project Forums CHARMM Interfaces MMTSB To generate unfolded conformations of protein at high T.

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.

Regards

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.

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 ?

@ 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.