From owner-chemistry@ccl.net Sat Jul 8 10:31:00 2006 From: "Kadir Diri kadir%visual1.chem.pitt.edu" To: CCL Subject: CCL: vibrational spectra with molden Message-Id: <-32089-060708000300-10921-URBrw1KF/OROkt16EolfrQ:server.ccl.net> X-Original-From: Kadir Diri Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=us-ascii Date: Fri, 07 Jul 2006 17:38:31 -0400 MIME-version: 1.0 Sent to CCL by: Kadir Diri [kadir],[visual1.chem.pitt.edu] Hello! I was wondering if one can change the x-tics interval (frequency) in spectra pictured by Molden. The default is to put a tic every 500 cm- which is not very helpfull in analyzing once printed out. Thanks! kadir From owner-chemistry@ccl.net Sat Jul 8 19:30:01 2006 From: "jitrayut jitonnom jitrayut.018]=[gmail.com" To: CCL Subject: CCL: peptide simulation before docking Message-Id: <-32090-060708164550-948-T08lkNJdpyCC7L2T68jD7A ~ server.ccl.net> X-Original-From: "jitrayut jitonnom" Content-Type: multipart/alternative; boundary="----=_Part_585_8377875.1152391528507" Date: Sun, 9 Jul 2006 03:45:28 +0700 MIME-Version: 1.0 Sent to CCL by: "jitrayut jitonnom" [jitrayut.018-*-gmail.com] ------=_Part_585_8377875.1152391528507 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear everybody, Actually, I am new for peptide docking and I have problems about docking peptide ligand (heptapeptide) to enzyme receptor (trypsin) by Autodock 3. To screening and finding the binding mode of 24 heptapeptides with autodock, it will take much cpu time to run according to blind docking (Hetenyi & Spoel et al). So, my questions is clasified in two cases; (1) For, heptapeptides ( no x-ray structure). How can I obtain the conformation of these peptides before docking? Actually, i have already done by AM1 semiempirical (Spartan '04) but I am not sure this is right because some papers use MD simulation ,but, did not tell much details (simulation time, implicit or explicit) on simulation, so I want some suggestions from anyone about setting the system for peptide simulation like this case. (2) For docking, I want to know that " Is there another way to screen this peptide complex by autodock",? Maybe can i reduce parameters such as ga_pop_size ,ga_num_eval, or ga_run for this system. Which are the appropriate parameters for the fast screening in this case? Thank in advance, Jitrayut Jitonnom, Ph.D.(candidate) Dept. of Chemistry, Computational Simulation, and Modeling Laboratory (CSML), Chiang Mai University, Thailand. Tel: +66(0)6613-4218 Email: jitrayut.018 a gmail.com ------=_Part_585_8377875.1152391528507 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear everybody,
 
Actually, I am new for peptide docking and I have problems about docking peptide ligand (heptapeptide) to enzyme receptor (trypsin) by Autodock 3. To screening and finding the binding mode of 24 heptapeptides with autodock, it will take much cpu time to run according to blind docking (Hetenyi & Spoel et al). So, my questions is clasified in two cases;
(1) For, heptapeptides ( no x-ray structure). How can I obtain the conformation of these peptides before docking? Actually, i have already done by AM1 semiempirical (Spartan '04) but I am not sure this is right because some papers use MD simulation ,but, did not tell much details (simulation time, implicit or explicit) on simulation, so I want some suggestions from anyone about setting the system for peptide simulation like this case.
(2) For docking, I want to know that " Is there another way to screen this peptide complex by autodock",? Maybe can i reduce parameters such as ga_pop_size ,ga_num_eval, or ga_run for this system. Which are the appropriate parameters for the fast screening in this case?
 
Thank in advance,
 
Jitrayut Jitonnom, Ph.D.(candidate)
Dept. of Chemistry,
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Tel: +66(0)6613-4218
Email: jitrayut.018 a gmail.com
 
 
 
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