From owner-chemistry@ccl.net Sat Aug 16 00:05:01 2014 From: "Mannan K malie_03 ~ yahoo.co.in" To: CCL Subject: CCL: Descriptors for peptides Message-Id: <-50402-140816000223-16638-070kFbdsCnN5V6NYnQ5SvQ__server.ccl.net> X-Original-From: "Mannan K" Date: Sat, 16 Aug 2014 00:02:21 -0400 Sent to CCL by: "Mannan K" [malie_03 ~~ yahoo.co.in] Hi CCLers, We have a list of peptides with a very little (only one) variation in their sequence (12mer), But they differ a lot in their solubility. Hence we would like to identify the descriptors which may be responsible for the specific properties, Small molecule could be straight forward, but the degrees of freedom are high with peptides .... How do we go from here, any suggestion would be of more help. Many Thanks, Mannan From owner-chemistry@ccl.net Sat Aug 16 09:08:01 2014 From: "ravinder suresh konda rkonda98|a|gmail.com" To: CCL Subject: CCL:G: Error termination in NtrErr: NtrErr called from FIOCnC. Message-Id: <-50403-140816061700-10022-G8+P54AvZJI+Jpiy+KJGLQ#server.ccl.net> X-Original-From: "ravinder suresh konda" Date: Sat, 16 Aug 2014 06:16:59 -0400 Sent to CCL by: "ravinder suresh konda" [rkonda98_+_gmail.com] hi sir while i am optimizing the 24 atom file by using the following path %mem=512mb # opt=(calcall,maxcycle=200) mp2/6-311++g(d,p) scf=(qc,maxcycle=2048) but i am getting the error dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 67072 FType=2 FMxFil=10000 Number 0 Base 20480 End 67072 End1 67072 Wr Pntr 20480 Rd Pntr 20480 Length 46592 Error termination in NtrErr: NtrErr called from FIOCnC. who to over come plz tell me 2Q:another qustion sir 24 atom file same path that can be optimized by Gaussian09 but Gaussian 03 is not showing the vibrational levels.so that's i taken the Gaussian 09 output file as a input file and i optimized than i am getting the Error termination in NtrErr: NtrErr called from FIOCnC. why and how to over come pl z tell me sir thank you Ravinder konda email:rkonda98%gmail.com School of Physical Sciences Swami Ramanand Teerth Marathwada University Nanded-431606 (Maharashtra-INDIA) From owner-chemistry@ccl.net Sat Aug 16 19:16:01 2014 From: "Reichert, David reichertd]~[mir.wustl.edu" To: CCL Subject: CCL: Need help Message-Id: <-50404-140815154639-12930-MHi2ESFT3KsWAFcdYA7kHw#,#server.ccl.net> X-Original-From: "Reichert, David" Content-ID: <7FE95554FC7129439CF3C14756B0927C#,#rad.wustl.edu> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 15 Aug 2014 19:46:31 +0000 MIME-Version: 1.0 Sent to CCL by: "Reichert, David" [reichertd[A]mir.wustl.edu] I usually use the program Chimera for those kinds of tasks, its freeware from UCSF. -david David E. Reichert Assoc. Professor of Radiology Washington University School of Medicine voice: (314) 362-8461 fax: (314) 362-9940 e-mail: reichertd:wustl.edu http://scoobie.wustl.edu/ On Aug 15, 2014, at 9:48 AM, Richard Wood richard.wood.:.purduecal.edu wrote: > > Sent to CCL by: "Richard Wood" [richard.wood{}purduecal.edu] > Hi all, > > Does anybody know of a free software tool that will allow the user to open a protein structure and place a small molecule (i.e., a ligand) anywhere the user wants it to be and then save the resulting structure for further calculations? > > I ask this because I am working with a ligand-protein system and I was trying to doc the ligand but it would not go where it was predicted to bind. I was trying to reproduce the work of others, but their protein was deemed "proprietary" but their institution and so I was using a different protein structure to start with. > > Richard> > ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. From owner-chemistry@ccl.net Sat Aug 16 21:10:00 2014 From: "Kerry Jeffry Wrighton-Araneda kerry.wrighton],[usach.cl" To: CCL Subject: CCL: Excitation Energies within a specific energy range Message-Id: <-50405-140816190929-8229-6u5dFZE0AXeoDNfgL2Ieew(0)server.ccl.net> X-Original-From: "Kerry Jeffry Wrighton-Araneda" Date: Sat, 16 Aug 2014 19:09:15 -0400 Sent to CCL by: "Kerry Jeffry Wrighton-Araneda" [kerry.wrighton-.-usach.cl] Dear CCL Suscribers: I have calculated excitation energies using TDDFT method included in g09 rev B.01. this calculation (nstate=180) give transition betwen 1500nm to about 400 nm, but I need to calculate a excitation energy within a specific energy range (200 - 400 nm), and after merge both calculations. 1- How to evaluate transition within a specific range? 2- Is it possible to merge both calculations in order to the whole spectra? 3- Can I use the first calculation checkfile to calculate transition between 200 and 400 nm? For any answers, please just send me an e-mail Best Regards