From owner-chemistry@ccl.net Sun Apr 26 03:01:00 2009 From: "Duy Le ttduyle/a\gmail.com" To: CCL Subject: CCL: WAVECAR of VASP Message-Id: <-39166-090426025838-29212-uWlhDK/N7XS3Dj6BU+iKgQ|*|server.ccl.net> X-Original-From: "Duy Le" Date: Sun, 26 Apr 2009 02:58:34 -0400 Sent to CCL by: "Duy Le" [ttduyle:+:gmail.com] Dear All, I spend lot of time to go thru VASP code to figure out the structure of WAVECAR. I need this wavefunction for post-work. However, it turns out that WAVECAR gives us only coefficient of Plan-Wave functions but without G-Vector. Unfortunately, I could not figure out those G-vectors. If anyone has any experience with this problem, please give me some tips. Thank all for reading. D. From owner-chemistry@ccl.net Sun Apr 26 11:02:00 2009 From: "mi yang agri_chemist(_)yahoo.com" To: CCL Subject: CCL: Diffuse function as a necessay evil Message-Id: <-39167-090426102438-26371-oL/7SbLb0LeeO3AiIAYYzg\a/server.ccl.net> X-Original-From: "mi yang" Date: Sun, 26 Apr 2009 10:24:33 -0400 Sent to CCL by: "mi yang" [agri_chemist^yahoo.com] Hello CCL colleagues, I want to discuss about basis set with diffuse function. Normally, with anionic or excess electron species during the calculation of CIS (Opt) or TD-DFT the diffuse function is consider essential but often it very difficultly converge the SCF (sometimes not at all) even with systems less than three benzene rings. Now My questions are: 1- I am dealing with optical properties of halogen ions (medium size systems) and often use 6-31+G* basis set in which diffuse function is often proves for me a necessary evil. Is there other equivalent basis set having diffuse function and also easy to converge in CIS or TD-DFT calculations? 2- Now my idea is How it would be If I will use the split basis set (Gen) I mean diffuse function for halogen ions only and without diffuse for other atoms in a system? Any related material or comment would be highly apriciated. Mi agri_chemist[#]yahoo.com From owner-chemistry@ccl.net Sun Apr 26 13:24:01 2009 From: "Jim Kress ccl_nospam%kressworks.com" To: CCL Subject: CCL: dimensionless normal coordinates Message-Id: <-39168-090426132207-2550-PiUtB0nmu9GwcB6mPcZufw-#-server.ccl.net> X-Original-From: "Jim Kress" Date: Sun, 26 Apr 2009 13:22:03 -0400 Sent to CCL by: "Jim Kress" [ccl_nospam++kressworks.com] Would anyone please point me to a reference (or provide me with a methodology, algorithm, or explanation) on how to calculate dimensionless normal coordinates given that I have the molecular hessian, force constant matrix and the vibrational frequencies for two states of a molecule? Thanks. Jim From owner-chemistry@ccl.net Sun Apr 26 14:14:00 2009 From: "Vincent.Leroux~~loria.fr" To: CCL Subject: CCL: GOLD_docking Message-Id: <-39169-090426135904-2914-RwpEagErFwFbICpQH7r4ng===server.ccl.net> X-Original-From: Vincent.Leroux,loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 26 Apr 2009 19:58:49 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux##loria.fr Hi Uzma, GOLD is very sensitive to input data consistency. You can run into =20 numerous problems, but I would first suggest you read the output log =20 files. These are particularly detailed and informative so take your =20 time. Some general advices - Is everything, target and ligands, protonated correctly? - Try to perform the calculation simply without the covalent bond =20 definition. If it launches fine, then you know exactly where the =20 problem is. - If your target protein is given as a PDB file, then GOLD converts it =20 automatically to MOL2 before processing it. Never did covalent docking =20 myself, but I would suggest, in such a case, double-checking the atom =20 numbers between the input and generated protein.mol2, as a mismatch =20 might translate to the covalent bond definition... - Make sure that your input ligands are in MOL2 format, and that the =20 atom types are correct. GOLD makes use of some non-standard =20 definitions, there is an entire section in the manual for that, check =20 it out. VL "uzma mahmood mehmoodchemist[*]gmail.com" a =E9cri= t=A0: > > Sent to CCL by: "uzma mahmood" [mehmoodchemist##gmail.com] > dear all subscriber > > any one can help me regarding docking on gold software by using =20 > covalent interaction all apply all the procedure as define in manual =20 > but i think i have some problem in input files so any one who has =20 > done this type of work so kindly help me resolve this problem > > > thanks > > uzma > From owner-chemistry@ccl.net Sun Apr 26 14:49:00 2009 From: "Dipankar Roy dipankarroy%a%iitb.ac.in" To: CCL Subject: CCL:G: Diffuse function as a necessay evil Message-Id: <-39170-090426140024-3497-aQUa0IikKpJmmXOjpmUtZw . server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8 Date: Sun, 26 Apr 2009 22:30:01 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy{=}iitb.ac.in] Hi, You can use Duuning's augmented basis sets. For Gaussian program, you can use Gen keyword for defining different basis set for different atoms. Gaussian web sites and manual contains detailed explanation for the same. Hope this may help, Dipankar Roy *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratory Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) *********************************************** WE ARE PERHAPS NOT FAR REMOVED FROM THE TIME WHEN WE SHALL BE ABLE TO SUBMITTHE BULK OF CHEMICAL PHENOMENA TO CALCULATION. -- JOSEPH LOUIS GAY-LUSSAC MEMOIRES DE LA SOCIETE D'ARCUEIL, 2, 207 (1808) From owner-chemistry@ccl.net Sun Apr 26 22:29:00 2009 From: "Jonas Baltrusaitis jonas-baltrusaitis~~uiowa.edu" To: CCL Subject: CCL: PHASE software Message-Id: <-39171-090426222659-6557-mfsPZe4eJ7ug6tGqeFLgDQ]|[server.ccl.net> X-Original-From: "Jonas Baltrusaitis" Date: Sun, 26 Apr 2009 22:26:55 -0400 Sent to CCL by: "Jonas Baltrusaitis" [jonas-baltrusaitis^-^uiowa.edu] Dear all, is anybody familiar with PHASE, a solid state software package created by a research group at National Inst. for Materials Science in Japan (Mr. Takahisa OHNO, project leader). It's an outstanding package and has an ultimate input creator/viewer/submitter. The biggest problem: no English manual and/or support forum (at least not that I know of). So I was wondering if anybody could share some light on that software and if an English manual can be retrieved or point of contact/mailing list/user forum thanks Jonas Baltrusaitis University of Iowa