From owner-chemistry@ccl.net Mon Aug 20 07:54:01 2007 From: "muhammad - shabbir asishabbir#%#gmail.com" To: CCL Subject: CCL:G: Optimization of molecule containing Ru hexa valence atom Message-Id: <-34953-070820053014-9822-8+4vcRJZBkwaSgsIpMiJ2Q^server.ccl.net> X-Original-From: "muhammad - shabbir" Date: Mon, 20 Aug 2007 05:30:07 -0400 Sent to CCL by: "muhammad - shabbir" [asishabbir-x-gmail.com] I am using Guassian03 and trying to optimize a molecule that has Ru as hexa valence and has about 60 atoms including C,N and H.I gave core potention to Ru,used LANL2DZ for Ru,increased no. of setps,Change converg=5 and rebuilt the structire again but still not succeded in optimizing that molecule.Please tell me some solution of this problem.I am giving some messages from failed out files: >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -1794.57682644 A.U. after 65 cycles Convg = 0.1829D-01 -V/T = 1.6784 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in e:\G98W\l502.exe Muhammad shabbir chemistry department NorthEast Normal university China E-mailID:asishabbir*gmail.com From owner-chemistry@ccl.net Mon Aug 20 10:49:01 2007 From: "Orlin Blajiev Orlin.Blajiev:vub.ac.be" To: CCL Subject: CCL: ONIOM with charge Message-Id: <-34954-070820103813-28531-fNepvFDDrYlCO3lYNImSxg**server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 20 Aug 2007 16:05:21 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [Orlin.Blajiev*_*vub.ac.be] Hi, I will appreciate if somebody explains me the following point. I try to calculate the adsorption parameters of an organic molecule on a Ag cluster. Cluster is itself embedded in a host of a Ag lattice. The molecule and the cluster are in the model and the rest of the Ag is accounted by UFF. Now , I would like to investigate the role of the charging of the cluster, but I want the charge to stay there and not to spread to the Ag lattice. When I do the charge multiplicity input, I say -1 2 -1 1 -1 1 which ( I think) means that a charge of -1 is confined to the model system during the model-high and model-low, but I suspect that charge of -1 distributes all over the real one during the real-low calculation. This would make the real quite different from what I expect. If this is true, is there any way to keep the charge in the model part during the calculation of the real-low? Best regards, Orlin -- Orlin Blajiev Materials and Chemistry (MACH) Dept. Metallurgy, Electrochemistry and Materials Science (META) Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev]~[vub.ac.be http://www.vub.ac.be/META ******************************************* ECASIA'07 will take place in Brussels, > from 09 to 14 September 2007 http://www.ecasia07.be ******************************************* From owner-chemistry@ccl.net Mon Aug 20 15:45:00 2007 From: "Matt Gave lazyamerican]=[gmail.com" To: CCL Subject: CCL:G: PBC Gaussian Calculations: Memory requirements Message-Id: <-34955-070820140942-32480-6On9GW8xymOeXjwl1Ej80Q---server.ccl.net> X-Original-From: "Matt Gave" Date: Mon, 20 Aug 2007 14:09:37 -0400 Sent to CCL by: "Matt Gave" [lazyamerican!^!gmail.com] I was wondering what kinds of systems people are using with PBC in Gaussian 03. My ultimate goal is to try and calculate NMR chemical shifts, but currently, even my single point energy calculations are crashing because of a lack of memory. Each time I run a calculation, it crashes as the dipole integrals are being calculated. Has anyone figured out a way around this limitation? Do I have any hope of getting chemical shift tensors out of Gaussian for a solid system? I know that there are problems with using pseudopotentials when calculating NMR chemical shifts, but I am not concerned with exact CSs and relative comparisons will suffice. Thanks in advance! ~Matt From owner-chemistry@ccl.net Mon Aug 20 16:20:01 2007 From: "Rajarshi Guha rguha^^indiana.edu" To: CCL Subject: CCL: Open Source 3D coordinate generation tool Message-Id: <-34956-070820151243-4635-T+6LV9hCwxrF9Va1bP/2Yw _ server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 20 Aug 2007 15:12:19 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha===indiana.edu] Hi, we have released a 3D coordinate generation tool called smi23d which will convert a SMILES string to a 3D structure. The program consists of two separate components: smi2sdf which converts a SMILES string to a 'rough' set of 3D coordinates using the stochastic proximity embedding (SPE) algorithm. Given the initial rough coordinates, the program called mengine then optimizes them using the MMFF94 forcefield to give a reasonable low energy structure. Note: these programs will only generate a single 3D structure. The code is written in C and is currently in the form of two standalone programs. In the future we plan to convert it to a library to ease inclusion within other systems. The software is released under the Apache 2.0 license. The program and instructions of compiling and usage can be obtained > from http://www.chembiogrid.org/cheminfo/smi23d/ At this point we have not performed significant benchmarking, mainly due to lack of access to other programs. However we welcome any comparisons with other programs and would be happy to help out in such efforts. We have used smi3d to convert about 99% of PubChem to 3D, the results of which are stored in a database which can be accessed at http:// www.chembiogrid.org/cheminfo/p3d/. ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Despite the high cost of living, it remains popular. From owner-chemistry@ccl.net Mon Aug 20 16:54:00 2007 From: "Yubo Fan yubofan{=}mail.chem.tamu.edu" To: CCL Subject: CCL: neutral ASP for docking Message-Id: <-34957-070820155255-20132-WYXd0PHle5xilLBvxRHofA*o*server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C7E339.BFB32C20" Date: Mon, 20 Aug 2007 14:52:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan_+_mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C7E339.BFB32C20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, I want to neutralize an aspartate residue in a docking job. Chimera is = used for the docking preparation. I guess the neutral aspartate is not = included in Chimera. Is there easy way to add a proton on the side chain = of the aspartate in Chimera? Thanks a lot, Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Yubo Fan Ph.D Email: yubofan^-^mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_0009_01C7E339.BFB32C20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, everyone,
 
I want to neutralize an aspartate = residue in a=20 docking job. Chimera is used for the docking preparation. I guess the = neutral=20 aspartate is not included in Chimera. Is there easy way to add a proton = on the=20 side chain of the aspartate in Chimera?
 
Thanks a lot,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Yubo=20 Fan =20 Ph.D           &nb= sp;=20 Email: yubofan^-^mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_0009_01C7E339.BFB32C20-- From owner-chemistry@ccl.net Mon Aug 20 17:30:02 2007 From: "Ivanciuc, Ovidiu I. oiivanci#%#utmb.edu" To: CCL Subject: CCL: Free solubility prediction software Message-Id: <-34958-070820160741-26506-DKwUDmLUpsr5uDvFVFM7BQ+/-server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 20 Aug 2007 15:07:21 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci[]utmb.edu] >>Is there any free software to calculate the solubility of small organic molecules? >>Any online web server on this point is also appreciated. Go to the Virtual Computational Chemistry Laboratory, http://www.vcclab.org/ and use ALOGPS, http://www.vcclab.org/lab/alogps/ ALOGPS computes the aqueous solubility from E-state topological indices and artificial neural networks. The dataset used to develop the solubility QSPR model is available from http://www.vcclab.org/lab/alogps/logs.txt and you may experiment with other machine learning models, such as support vector machines - for a list of SVM software see the review "Applications of Support Vector Machines in Chemistry" http://www.ivanciuc.org/Files/Reprint/Ivanciuc_SVM_CCR_2007_23_291.pdf and http://www.support-vector-machines.org/ Regards, Ovidiu From owner-chemistry@ccl.net Mon Aug 20 23:10:00 2007 From: "LI Daobing lidaobing+ccl * gmail.com" To: CCL Subject: CCL:G: PBC Gaussian Calculations: Memory requirements Message-Id: <-34959-070820200950-16810-Yc+P+/ReSp2XbJxlojiQ3w||server.ccl.net> X-Original-From: "LI Daobing" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 21 Aug 2007 07:10:12 +0800 MIME-Version: 1.0 Sent to CCL by: "LI Daobing" [lidaobing+ccl[-]gmail.com] On 8/21/07, Matt Gave lazyamerican]=[gmail.com wrote: > > Sent to CCL by: "Matt Gave" [lazyamerican!^!gmail.com] > I was wondering what kinds of systems people are using with PBC in Gaussian 03. My ultimate goal is to try and calculate NMR chemical shifts, but currently, even my single point energy calculations are crashing because of a lack of memory. > > Each time I run a calculation, it crashes as the dipole integrals are being calculated. Has anyone figured out a way around this limitation? Do I have any hope of getting chemical shift tensors out of Gaussian for a solid system? I know that there are problems with using pseudopotentials when calculating NMR chemical shifts, but I am not concerned with exact CSs and relative comparisons will suffice. > I think you should try materials studio instead of gaussian -- LI Daobing