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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 30
- To: Ashish Runthala <ashishr AT bits-pilani.ac.in>
- Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 30
- From: Alexander Predeus <predeus AT gmail.com>
- Date: Sat, 17 Mar 2012 02:58:22 -0400
- Cc: modeller_usage@listsrv.ucsf.edu
Dear Ashish,
thank you for your suggestions! I have some follow-up questions though.
1. Did you mean some simplified replica exchange with MODELLER or a real replica-exchange simulation? Because simple temperature replica exchange is most probably not feasible for a system of this size - number of replicas necessary to achieve the same exchange rates grows as ~ sqrt (N) and will be too high in this case.
2. As for increased temperature MD for loops - you imply that I keep the structure restrained and only let loops relax? I was under the impression MODELLER's refinement does something of this sort in CG model, which should be a lot faster than AA MD anyway.
3. About the normalized DOPE - again, I was under the impression that it only matters when you are comparing different proteins. My task is only to compare different models of the same protein.
Thank you in advance!
-- Alex Predeus,
MSU