From owner-chemistry@ccl.net Tue Dec 5 04:51:01 2006 From: "Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com" To: CCL Subject: CCL: Freeware for building peptides Message-Id: <-33172-061205043757-22638-taquGaRCuZgQZdOp2wtNPA^^^server.ccl.net> X-Original-From: "Itna Kcolc" Date: Tue, 5 Dec 2006 04:37:57 -0500 Sent to CCL by: "Itna Kcolc" [a_n_t_i_c_l_o_c_k(0)yahoo.com] Hello CCLers, I'm looking for a freewrare for windows/linux( an web server will do too) to build up peptides,particularly small helical peptides similar to what ACCELRYS BIOPOLYMER module can do. Thanks in advance From owner-chemistry@ccl.net Tue Dec 5 06:38:00 2006 From: "Gijs Schaftenaar schaft[A]cmbi.ru.nl" To: CCL Subject: CCL: Freeware for building peptides Message-Id: <-33173-061205060422-17047-1GVZF2h8ZYMk/aluPRPKRQ[#]server.ccl.net> X-Original-From: Gijs Schaftenaar Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 5 Dec 2006 11:22:42 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Gijs Schaftenaar [schaft()cmbi.ru.nl] Dear Itna, Molden can do this (URL: http://www.cmbi.ru.nl/molden) Start molden without an input file -> click "Z-matrix editor" -> click "Substitute atom by Fragment" -> choose "Sequence" -> specify the sequence by cliking the residue buttons, choose the secondary sructure type and click "Build", you can still change Phi, Psi and Chi1-4 dihedral angles in the Zmatrix editor window. Best Regards, Gijs Schaftenaar +----------------------------------------------------------------+ Gijs Schaftenaar, Dr. | Computational Drug Discovery, CMBI Email: | Radboud University of Nijmegen G.Schaftenaar,,ncmls.ru.nl | Medical Centre / NCMLS, route 260 Tel. : +31 24 3619674 | Geert-Grooteplein 28 Fax : +31 24 3619395 | 6525 GA Nijmegen, The Netherlands +----------------------------------------------------------------+ On Tue, 5 Dec 2006, Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com wrote: > Date: Tue, 5 Dec 2006 05:00:45 -0500 > From: "Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com" > Reply-To: CCL Subscribers > To: "Schaftenaar, Gijs " > Subject: CCL: Freeware for building peptides > > Sent to CCL by: "Itna Kcolc" [a_n_t_i_c_l_o_c_k(0)yahoo.com] > Hello CCLers, > > I'm looking for a freewrare for windows/linux( an web server will do > too) to build up peptides,particularly small helical peptides similar to what ACCELRYS BIOPOLYMER module can do. > > Thanks in advance> > > From owner-chemistry@ccl.net Tue Dec 5 07:39:00 2006 From: "Carl LeBlond carl.leblond(0)iup.edu" To: CCL Subject: CCL:G: Diradicaloid Transition State Message-Id: <-33174-061204211558-13389-TG2+hfTb0BVGEE5Z/JcNBA_-_server.ccl.net> X-Original-From: "Carl LeBlond" Date: Mon, 4 Dec 2006 21:15:58 -0500 Sent to CCL by: "Carl LeBlond" [carl.leblond(0)iup.edu] Thanks to Cory, Wai-To and Daria. Your help was greatly appreciated. Following Cory's lead I got the TS I was looking for using Gaussian. I have been searching through the GAMESS manual in hopes of finding the correct keywords to do the same. Is WF stability/optimization in GAMESS(US) not possible? Cheers! Carl From owner-chemistry@ccl.net Tue Dec 5 08:35:00 2006 From: "sanjay kumar computationalchemist~~gmail.com" To: CCL Subject: CCL: conversion of sec to atomic units Message-Id: <-33175-061205083353-17892-Sn8pi/0nunbLS8NzEJnLuQ::server.ccl.net> X-Original-From: "sanjay kumar" Date: Tue, 5 Dec 2006 08:33:52 -0500 Sent to CCL by: "sanjay kumar" [computationalchemist ~ gmail.com] hi all, I know this is a naive question, but struggling since morning. can you pleze let me know the conversion factor for converting seconds to atomic units. thanks and regards, dr. sanjay From owner-chemistry@ccl.net Tue Dec 5 09:10:00 2006 From: "CCL CCL computationalchemist__gmail.com" To: CCL Subject: CCL: conversion of seconds to atomic mass units Message-Id: <-33176-061205084455-16255-SoR0Y54P1oRXGVeU6GOPBQ*_*server.ccl.net> X-Original-From: "CCL CCL" Content-Type: multipart/alternative; boundary="----=_Part_6546_26040142.1165322825902" Date: Tue, 5 Dec 2006 12:47:05 +0000 MIME-Version: 1.0 Sent to CCL by: "CCL CCL" [computationalchemist%gmail.com] ------=_Part_6546_26040142.1165322825902 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline dear folks, I know this is very naive question, but still i couldnt get answer. I'm wondering how to convert seconds to atomic mass units. Any suggestions will be greatly appreciated. -- Regards, Dr. Sanjay ------=_Part_6546_26040142.1165322825902 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
dear folks,
I know this is very naive question, but still i couldnt get answer. I'm wondering how to convert seconds to atomic mass units.
Any suggestions will be greatly appreciated.
--
Regards,
Dr. Sanjay
------=_Part_6546_26040142.1165322825902-- From owner-chemistry@ccl.net Tue Dec 5 09:45:00 2006 From: "Georg Lefkidis lefkidis:+:physik.uni-kl.de" To: CCL Subject: CCL: conversion of sec to atomic units Message-Id: <-33177-061205092122-15191-nHCzSi2HiWVWoDdFG5ufgA%%server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 5 Dec 2006 14:43:46 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis-$-physik.uni-kl.de] Dear Kumar, The following site has all possible conversions http://folk.uio.no/michalj/node72.html To convert n seconds to a.u. multiply n by 4.1341 x 10^16. Cheers George --------------------------------------------------------------- Dr. Georg Lefkidis E-mail:lefkidis ~ physik.uni-kl.de University of Kaiserslautern Tel. +49 631 205 3207 Department of Physics Fax: +49 631 205 3907 PO Box 3049 67653 Kaiserslautern Germany --------------------------------------------------------------- > -----Ursprüngliche Nachricht----- > Von: owner-chemistry ~ ccl.net [mailto:owner-chemistry ~ ccl.net] > Gesendet: Dienstag, 5. Dezember 2006 14:37 > An: Lefkidis, Georg > Betreff: CCL: conversion of sec to atomic units > > > Sent to CCL by: "sanjay kumar" [computationalchemist ~ gmail.com] > hi all, > I know this is a naive question, but struggling since morning. > can you pleze let me know the conversion factor for converting > seconds to atomic units. > thanks and regards, > dr. sanjay> > > > -- > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.5.430 / Virus Database: 268.15.7/569 - Release Date: > 05/12/06 03:00 > -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.430 / Virus Database: 268.15.7/569 - Release Date: 05/12/06 03:00 From owner-chemistry@ccl.net Tue Dec 5 10:19:01 2006 From: "T. Daniel Crawford crawdad=exchange.vt.edu" To: CCL Subject: CCL: conversion of sec to atomic units Message-Id: <-33178-061205092254-15388-3Nj2zZwvCfCCfgRczsR8PQ++server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Tue, 05 Dec 2006 09:22:47 -0500 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad]_[exchange.vt.edu] Sanjay, Please see: http://en.wikipedia.org/wiki/Atomic_units -Daniel On 12/5/06 8:47 AM, "sanjay kumar computationalchemist~~gmail.com" wrote: > Sent to CCL by: "sanjay kumar" [computationalchemist ~ gmail.com] > hi all, > I know this is a naive question, but struggling since morning. can you pleze > let me know the conversion factor for converting seconds to atomic units. > thanks and regards, > dr. sanjay > -- T. Daniel Crawford Department of Chemistry crawdad^vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From owner-chemistry@ccl.net Tue Dec 5 10:55:01 2006 From: "Dimitrios A. Pantazis d.pantazis a chem.gla.ac.uk" To: CCL Subject: CCL: conversion of seconds to atomic mass units Message-Id: <-33179-061205094138-22853-IFAO5BljFp7OwT1NiWRXNA[]server.ccl.net> X-Original-From: "Dimitrios A. Pantazis" Date: Tue, 5 Dec 2006 09:41:38 -0500 Sent to CCL by: "Dimitrios A. Pantazis" [d.pantazis.:.chem.gla.ac.uk] >Sent to CCL by: "CCL CCL" [computationalchemist%gmail.com] >dear folks, >I know this is very naive question, but still i couldnt get answer. I'm >wondering how to convert seconds to atomic mass units. >Any suggestions will be greatly appreciated. >-- >Regards, >Dr. Sanjay According to NIST, 1 a.u. of time is equivalent to 24.188843265x10^(-18) seconds. Dimitrios ---- Dr. Dimitrios A. Pantazis Computational Chemistry Group WestCHEM, Department of Chemistry Joseph Black Building University of Glasgow Glasgow G12 8QQ United Kingdom Telephone: +44 (0)141 330 8121 E-mail: d.pantazis^chem.gla.ac.uk Web: http://www.chem.gla.ac.uk/staff/dimitp ---- From owner-chemistry@ccl.net Tue Dec 5 11:30:00 2006 From: "Jens Spanget-Larsen spanget * ruc.dk" To: CCL Subject: CCL: conversion of sec to atomic units Message-Id: <-33180-061205094924-30811-UD4WOf3lUC3XjU5Y/GXvvA/./server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Dec 2006 15:49:22 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget++ruc.dk] Dear Dr. Sanjay, according to IUPAAC [1], one atomic unit of time is equal to h(bar)/Eh. Here h(bar) is Planck's constant divided by 2*pi (h(bar) = 1.0546*10^(-34) J s). Eh is the atomic unit of energy (Eh = 4.3598*10^(-18) J). Hence, one atomic unit of time amounts to 2.4189*10^(-17) seconds. Yours, Jens >--< [1] D. H. Whiffen, Pure & Appl. Chem., Vol 50, pp 75-79 (1978). ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget|a|ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ sanjay kumar computationalchemist~~gmail.com wrote: > Sent to CCL by: "sanjay kumar" [computationalchemist ~ gmail.com] > hi all, > I know this is a naive question, but struggling since morning. can you pleze let me know the conversion factor for converting seconds to atomic units. > thanks and regards, > dr. sanjay From owner-chemistry@ccl.net Tue Dec 5 12:04:01 2006 From: "Giulio Vistoli giulio.vistoli(~)unimi.it" To: CCL Subject: CCL: Freeware for building peptides Message-Id: <-33181-061205065142-7210-JFyKs65igYhOLBw3p6ydlQ+/-server.ccl.net> X-Original-From: Giulio Vistoli Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=iso-8859-1; reply-type=original Date: Tue, 05 Dec 2006 11:50:08 +0100 MIME-version: 1.0 Sent to CCL by: Giulio Vistoli [giulio.vistoli%a%unimi.it] Dear CCLers, VEGAZZ software (free downloadable at www.ddl.unimi.it) includes a molecular builder which can build peptides using both L and D residues and selecting the phi&psi angles Best regards Giulio Vistoli ----- Original Message ----- > From: "Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com" To: "Vistoli, Giulio " Sent: Tuesday, December 05, 2006 11:07 AM Subject: CCL: Freeware for building peptides > Sent to CCL by: "Itna Kcolc" [a_n_t_i_c_l_o_c_k(0)yahoo.com] > Hello CCLers, > > I'm looking for a freewrare for windows/linux( an web server will do > too) to build up peptides,particularly small helical peptides similar to > what ACCELRYS BIOPOLYMER module can do. > > Thanks in advance> > > > From owner-chemistry@ccl.net Tue Dec 5 12:40:01 2006 From: "Wai-To Chan chan]^[curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: Diradicaloid Transition State Message-Id: <-33182-061205113052-28561-ALyIErVk+R1PnUcRnOFAgw+*+server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 5 Dec 2006 11:36:54 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan**curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<<<<< Sent to CCL by: "Carl LeBlond" [carl.leblond(0)iup.edu] Thanks to Cory, Wai-To and Daria. Your help was greatly appreciated. Following Cory's lead I got the TS I was looking for using Gaussian. I have been searching through the GAMESS manual in hopes of finding the correct keywords to do the same. Is WF stability/optimization in GAMESS(US) not possible? Cheers! Carl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GAMESS-US does not have a stability code. To obtain a broken-symmetry UHF solution you have to specify SCFTYP=UHF in $CONTRL and MIX=.TRUE. in $GUESS. If the spin-symmetry remains intact (zero spin contamination and equal UHF and RHF energy) or SCF simply fails to converge add the following keywords: $SCF DAMP=.TRUE. NOCONV=.TRUE. $END This will turn off DIIS and turn on dampinp which is generally more reliable. Also specify a larger number of SCF scycles in $CONTRL with MAXIT=xxx. The above keywords usually works from my experience. If the structure has symmetry you may need to specify a C1 symmetry. It is possible that convergence to the same stable UHF energy of Gaussian is not attained in a single job however large the number of SCF cycles are. I often ended up having to repeat the SCF step with the unconverged MO as the initial guess to obtain a stable UHF solution in a subsequent job. Wai-To Chan From owner-chemistry@ccl.net Tue Dec 5 13:15:01 2006 From: "Igor Filippov Contr igorf,helix.nih.gov" To: CCL Subject: CCL: conversion of seconds to atomic mass units Message-Id: <-33183-061205114404-12506-nBkAMdlhYIDR4+1e5eSIDQ^-^server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 05 Dec 2006 11:43:16 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf:+:helix.nih.gov] Yes, but Dr. Sanjay is asking to convert seconds to _mass_ units. Anybody can convert time units to time units. Time to mass conversion is somewhat less trivial ! Igor > >wondering how to convert seconds to atomic mass units. > >Any suggestions will be greatly appreciated. > >-- > >Regards, > >Dr. Sanjay > > According to NIST, 1 a.u. of time is equivalent to 24.188843265x10^(-18) seconds. > > Dimitrios From owner-chemistry@ccl.net Tue Dec 5 14:00:00 2006 From: "Shobe, David David.Shobe[*]sud-chemie.com" To: CCL Subject: CCL: conversion of seconds to atomic mass units Message-Id: <-33184-061205135703-6982-EB+uiOpNuFoxdqAKjHQr8g^server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Dec 2006 19:51:01 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe]~[sud-chemie.com] The relation of time to mass is actually inverse, as the following sleight of hand proves: 1 amu = 931.494 x 10^6 eV 1 eV = 36.7502 x 10^-3 hartrees 1 hartree = 219.474 x 10^3 cm^-1 1 cm^-1 = 29.9793 x 10^9 Hz 1 Hz = 1 sec^-1 Thus, 1 amu = 225.239 x 10^21 sec-1 ;-) --David Shobe -----Original Message----- > From: owner-chemistry]~[ccl.net [mailto:owner-chemistry]~[ccl.net] Sent: Tuesday, December 05, 2006 1:16 PM To: Shobe, David Subject: CCL: conversion of seconds to atomic mass units Sent to CCL by: "Igor Filippov [Contr]" [igorf:+:helix.nih.gov] Yes, but Dr. Sanjay is asking to convert seconds to _mass_ units. Anybody can convert time units to time units. Time to mass conversion is somewhat less trivial ! Igor > >wondering how to convert seconds to atomic mass units. > >Any suggestions will be greatly appreciated. > >-- > >Regards, > >Dr. Sanjay > > According to NIST, 1 a.u. of time is equivalent to 24.188843265x10^(-18) seconds. > > Dimitrioshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Tue Dec 5 14:35:00 2006 From: "M. L. Dodson mldodson]*[houston.rr.com" To: CCL Subject: CCL: Freeware for building peptides Message-Id: <-33185-061205131604-19609-P6P68+IwZqitSuz5GIVBTA^_^server.ccl.net> X-Original-From: "M. L. Dodson" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 5 Dec 2006 12:16:01 -0600 MIME-Version: 1.0 Sent to CCL by: "M. L. Dodson" [mldodson-x-houston.rr.com] On Tuesday 05 December 2006 04:01, Itna Kcolc a_n_t_i_c_l_o_c_k,,yahoo.com wrote: > Sent to CCL by: "Itna Kcolc" [a_n_t_i_c_l_o_c_k(0)yahoo.com] > Hello CCLers, > > I'm looking for a freewrare for windows/linux( an web server will do > too) to build up peptides,particularly small helical peptides similar to > what ACCELRYS BIOPOLYMER module can do. > > Thanks in advance > > This may be more than you want, but if you install nab (http://www.scripps.edu/mb/case/, GPL licensed) from the Dave Case lab, you also get peptide, written by Paul Beroza in the nab language, as one of the supplied example utility programs. peptide will generate a structure (PDB file) given a sequence and a secondary structure specification: alpha helix, beta sheet, various turns (I counted 13 types of turns), etc. New types are easy to add by simply editing a configuration file. Bud Dodson PS, nab is an incredibly useful "molecular manipulation language", a kind of modified C with, e.g., molecule and atom as primitive variable types. -- M. L. Dodson Email: mldodson-at-houston-dot-rr-dot-com Phone: eight_three_two-56_three-386_one From owner-chemistry@ccl.net Tue Dec 5 15:10:00 2006 From: "Matt Thompson thompsma,jilau1.colorado.edu" To: CCL Subject: CCL: conversion of seconds to atomic mass units Message-Id: <-33186-061205143521-28872-bpIXV2T4DnZqxEt+U50tGw^_^server.ccl.net> X-Original-From: Matt Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Tue, 05 Dec 2006 11:49:21 -0700 MIME-Version: 1.0 Sent to CCL by: Matt Thompson [thompsma~!~jilau1.colorado.edu] The heavens stretched forth and Igor Filippov Contr igorf,helix.nih.gov decreed the following on or about 12/05/2006 11:20 AM: > Sent to CCL by: "Igor Filippov [Contr]" [igorf:+:helix.nih.gov] > Yes, but Dr. Sanjay is asking to convert seconds to _mass_ units. > Anybody can convert time units to time units. Time to mass conversion is > somewhat less trivial ! Well, just by looking at units, wouldn't E_h/(a_0 * c) provide kilograms > from seconds? So 1 s = 2.748142E-16 kg ? (no error propagation here...) Matt -- The mayfly lives only one day, and sometimes it rains. - Geo. Carlin Matt Thompson -- http://ucsub.colorado.edu/~thompsma/ 440 UCB, Boulder, CO 80309-0440 JILA A510, 303-492-4662 From owner-chemistry@ccl.net Tue Dec 5 16:24:00 2006 From: "Wai-To Chan chan-,-curl.gkcl.yorku.ca" To: CCL Subject: CCL: conversion of seconds to atomic mass units Message-Id: <-33187-061205162118-10177-fQHTY0kxPjhhzYV5YFtj+g-$-server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 5 Dec 2006 16:27:22 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan : curl.gkcl.yorku.ca] <<<<<<<<<<<< So 1 s = 2.748142E-16 kg ? (no error propagation here...) >>>>>>>>>>>>>>>>>>> Only if you change the number of fundamental dimensions from four to three. It used to be: mass, length, time and charge. One of time and mass can now be taken away. The law of conservation of energy was at some time modified to become the law of conservation of energy and mass. An update to the law of conservation of energy, mass and time is overdue. Wai-To Chan