From owner-chemistry@ccl.net Wed Aug 16 09:32:00 2017 From: "Bala Chandramouli bala.biophysics#%#gmail.com" <owner-chemistry+*+server.ccl.net> To: CCL Subject: CCL: Montecarlo dihedral moves Message-Id: <-52925-170816060748-20602-tpwHT1LZUj6B5qg7uHYUSA+*+server.ccl.net> X-Original-From: "Bala Chandramouli" <bala.biophysics . gmail.com> Date: Wed, 16 Aug 2017 06:07:47 -0400 Sent to CCL by: "Bala Chandramouli" [bala.biophysics[#]gmail.com] Dear CCL users, I have to perform a conformational sampling with montecarlo. In brief, I have to generate montecarlo moves on several dihedrals in my molecule. To this end, I thought of two options; a) randomly generate the dihedrals between -180 to 180 (which means doing random jumps in the phase space) or b) start with several random initial conformations of the molecule and then make small random moves to the starting dihedral values in order to sample the phase space closer to nearby local minima. Please give me some expert opinion on this issue. I would also appreciate any reference articles on this line. Best, Bala From owner-chemistry@ccl.net Wed Aug 16 11:33:00 2017 From: "Mezei, Mihaly mihaly.mezei]_[mssm.edu" <owner-chemistry%server.ccl.net> To: CCL Subject: CCL: Montecarlo dihedral moves Message-Id: <-52926-170816113138-20581-EcPAruBmMLVdpObB+93CAA%server.ccl.net> X-Original-From: "Mezei, Mihaly" <mihaly.mezei _ mssm.edu> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 16 Aug 2017 15:31:32 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei : mssm.edu] Greetings, here is a relevant reference (open access): J.R. Banfelder, J.A. Speidel, and M. Mezei, Automatic determination of stepsize parameters in Monte Carlo simulations, tested on a bromodomain-binding octapeptide, Algorithms, 2, 215-226 (2009); DOI:10.3390/a2010215 Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://www.mssm.edu/departments-and-institutes/pharmacology-and-systems-therapeutics ________________________________________ > From: owner-chemistry+mihaly.mezei==mssm.edu^^ccl.net [owner-chemistry+mihaly.mezei==mssm.edu^^ccl.net] on behalf of Bala Chandramouli bala.biophysics#%#gmail.com [owner-chemistry^^ccl.net] Sent: Wednesday, August 16, 2017 6:07 AM To: Mezei, Mihaly Subject: CCL: Montecarlo dihedral moves Sent to CCL by: "Bala Chandramouli" [bala.biophysics[#]https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=vGi9-AWpOf9aE-G2lNksthYfQY0swP9Hu-8he-O68AQ&e= ] Dear CCL users, I have to perform a conformational sampling with montecarlo. In brief, I have to generate montecarlo moves on several dihedrals in my molecule. To this end, I thought of two options; a) randomly generate the dihedrals between -180 to 180 (which means doing random jumps in the phase space) or b) start with several random initial conformations of the molecule and then make small random moves to the starting dihedral values in order to sample the phase space closer to nearby local minima. Please give me some expert opinion on this issue. I would also appreciate any reference articles on this line. Best, Balahttps://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_cgi-2Dbin_ccl_send-5Fccl-5Fmessage&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=2AtWGyWixYlJa-luoGJVoWSSZX9kQD07tTk96r7EDD0&e=https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_cgi-2Dbin_ccl_send-5Fccl-5Fmessage&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=2AtWGyWixYlJa-luoGJVoWSSZX9kQD07tTk96r7EDD0&e=https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_chemistry_sub-5Funsub.shtml&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=oo2FQ29k88aemz7bwtAhGifXUFeDInmuL3eDo_8Re6M&e= Before posting, check wait time at: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=J844F4woWPBQcy79YslWD4RbqCVJVJGnTLvacsDfKX0&e= Job: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_jobs&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=dJkwUEOWuuyZqHrSbUiWywFlefYtRGG8e217PR8xkrU&e= Conferences: https://urldefense.proofpoint.com/v2/url?u=http-3A__server.ccl.net_chemistry_announcements_conferences_&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=vOVdxh2Eag5ekFoKYm1BEdi9mJ55QKKuZ-VBrHXY7SA&e= Search Messages: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_chemistry_searchccl_index.shtml&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=fnLH0sRKmxaFy4hxXFWclqENE6eBvtc5IYXpLllM98g&e=https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_spammers.txt&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=IK4NDjJQUdU4wGOWk3Ts3OTb5ewjeEPvQ5qjlU7dL1c&e= RTFI: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccl.net_chemistry_aboutccl_instructions_&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=mw0wcCoXmR7oKiTKaPyVkT_3PoT9eJAN4PTGFSpqZhk&s=QsKPzNncEx8mdfxzQsgSM7UTsFvmkujaL4_KFUUBgS0&e= From owner-chemistry@ccl.net Wed Aug 16 12:32:00 2017 From: "Joshua T Berryman josh.berryman]![uni.lu" <owner-chemistry^^^server.ccl.net> To: CCL Subject: CCL: Montecarlo dihedral moves Message-Id: <-52927-170816123102-30923-/n+rnl42+cAlhRljHL8bEg^^^server.ccl.net> X-Original-From: "Joshua T Berryman" <josh.berryman]~[uni.lu> Date: Wed, 16 Aug 2017 12:31:01 -0400 Sent to CCL by: "Joshua T Berryman" [josh.berryman===uni.lu] There are a few tools around for moving between discrete conformations of peptide chains based on flipping dihedrals around the Ramachandran plane. Top google hit is: http://www.moleculesinaction.com/pdmd.html A good much-overlooked paper (Clarke and Parker) is here: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21085/full When you have tried a few things, why not send a follow-up post to say how you got on? Josh Berryman Uni Luxembourg