To the list, and especially the original poster:

I finally did something I should have done earlier, and checked the publis= hed literature. :-)

It does turn out to be a much more dif= ficult computational chemistry problem than it looks!

Electronic structures of Pd4 and Pt4


&n= bsp;
Electronic structures of Pd4 and P= t4 Complete active space multiconfiguration self=E2=80= =90consistent field (CAS=E2=80=90MCSCF) followed by multireference configur= ation interaction computations which included up to 4.1 million configurati= ons and correlated all 40 electrons of Pd4 and Pt4 were made. Relativistic = effective core potent...

View on scitation.aip.org	Preview by Ya= hoo

--David Shobe

------=_Part_1157191_1964033789.1456819819752-- From owner-chemistry@ccl.net Tue Mar 1 07:00:00 2016 From: "J C Womack jw5533%%my.bristol.ac.uk" To: CCL Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52085-160301065732-17062-XUQEXHVlfzNF6nv+aLCCkQ.:.server.ccl.net> X-Original-From: J C Womack Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Tue, 1 Mar 2016 11:57:25 +0000 MIME-Version: 1.0 Sent to CCL by: J C Womack [jw5533^-^my.bristol.ac.uk] It is also worth considering the possibility that the meta-GGA exchange functional (M06-L) itself is misbehaving. It is known that certain meta-GGAs (including M06-L) produce singularities for some electron densities, resulting in SCF convergence problems. See for example: Gr�fenstein, J., Izotov, D. & Cremer, D. Avoiding singularity problems associated with meta-GGA (generalized gradient approximation) exchange and correlation functionals containing the kinetic energy density. The Journal of Chemical Physics 127, 214103 (2007). http://scitation.aip.org/content/aip/journal/jcp/127/21/10.1063/1.2800011 Regards, James On 26/02/16 05:12, Bulumoni Kalita bulumoni:dibru.ac.in wrote: > Sent to CCL by: "Bulumoni Kalita" [bulumoni- -dibru.ac.in] > Dear CCL users, > I have optimized tetrahedral structure of Pd4 cluster in (UB3LYP/LANL2DZ) level in Gaussian 09. I wanted to repeat the calculation in (UM06L/LANL2DZ) level. However, SCF is not converging in this case. Rather it is fluctuating between to range of values. I have tried using SCF(xqc, maxcycle=500), opt(maxcycle=500) etc. > > Please give your valuable suggestions to overcome this problem.> > -- James C. Womack Email: jw5533_-_my.bristol.ac.uk Web: http://jcwomack.uk From owner-chemistry@ccl.net Tue Mar 1 10:26:01 2016 From: "Daniel Roe daniel.r.roe ~~ gmail.com" To: CCL Subject: CCL: Overlay structure Message-Id: <-52086-160301102419-17307-V6NwxOS8y3D/m3MROdJqeA+*+server.ccl.net> X-Original-From: Daniel Roe Content-Type: text/plain; charset=UTF-8 Date: Tue, 1 Mar 2016 08:24:13 -0700 MIME-Version: 1.0 Sent to CCL by: Daniel Roe [daniel.r.roe|gmail.com] Hi, If you would like a scriptable way to do this you could use CPPTRAJ, part of the freely available AmberTools (http://ambermd.org/AmberTools15-get.html). For example, if your X-ray structure is called X-ray.pdb and your optimized structure is called Opt.pdb, you could use the following commands in CPPTRAJ to perform a best-fit alignment and calculate RMSD for all CA atoms: parm X-ray.pdb reference X-ray.pdb trajin Opt.pdb rms ToRef reference ]_[CA out rmsd.dat trajout Aligned.pdb go The structure of Opt.pdb aligned on X-ray.pdb will be written to Aligned.pdb, and the RMSD will be written to 'rmsd.dat'. You can also calculate the per-residue RMSD if desired via the 'perres' keyword. Hope this helps, -Dan On Mon, Feb 29, 2016 at 12:34 PM, Saied Mohammed Soliman saied1soliman%yahoo.com wrote: > > Sent to CCL by: "Saied Mohammed Soliman" [saied1soliman__yahoo.com] > Hello colleagues, > I need a free and user friendly software to overlay the optimized structure > with the X-ray structure in order to compare the matching between them, > anyone could help me. > Thanks > Saied> > -- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) From owner-chemistry@ccl.net Tue Mar 1 14:03:00 2016 From: "Elaine C Meng meng#%#cgl.ucsf.edu" To: CCL Subject: CCL: Overlay structure Message-Id: <-52087-160229193151-7883-SMt4bpimyqjN4NEK0vZBLw() server.ccl.net> X-Original-From: "Elaine C Meng" Date: Mon, 29 Feb 2016 19:31:50 -0500 Sent to CCL by: "Elaine C Meng" [meng _ cgl.ucsf.edu] Hi Saied, Im sure there are many programs that can do this, but one is UCSF Chimera, which is a free download for noncommercial use. You can just open the two PDB files (menu: File Open) and then use the MatchMaker tool to superimpose them (menu: Tools Structure Comparison MatchMaker). The dialog has lots of options, but you can just leave them alone to try the defaults. Just choose one structure as the reference and the other as the structure to match, then click the OK button at the bottom. If you think the overlay could be improved, you can always try again with different MatchMaker settings, but usually the defaults work quite well. UCSF Chimera homepage (see download in quick links on left) http://www.rbvi.ucsf.edu/chimera/index.html MatchMaker description http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html After the structure to match is overlaid on the other satisfactorily, you can save a new PDB file of that position, menu: File Save PDB. Choose the option to save it relative to the other, reference structure. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Tue Mar 1 19:57:01 2016 From: "Susi Lehtola susi.lehtola^^alumni.helsinki.fi" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52088-160301123754-23630-PX9XiJUHVewUsO9sAWATgw[-]server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 1 Mar 2016 09:37:39 -0800 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola- -alumni.helsinki.fi] On 03/01/2016 03:57 AM, J C Womack jw5533%%my.bristol.ac.uk wrote: > > Sent to CCL by: J C Womack [jw5533^-^my.bristol.ac.uk] > It is also worth considering the possibility that the meta-GGA exchange > functional (M06-L) itself is misbehaving. > > It is known that certain meta-GGAs (including M06-L) produce > singularities for some electron densities, resulting in SCF convergence > problems. See for example: > > Gr�fenstein, J., Izotov, D. & Cremer, D. Avoiding singularity problems > associated with meta-GGA (generalized gradient approximation) exchange > and correlation functionals containing the kinetic energy density. The > Journal of Chemical Physics 127, 214103 (2007). > http://scitation.aip.org/content/aip/journal/jcp/127/21/10.1063/1.2800011 Minnesota density functionals are known to be numerically problematic, see also N. Mardirossian and M. Head-Gordon, Characterizing and Understanding the Remarkably Slow Basis Set Convergence of Several Minnesota Density Functionals for Intermolecular Interaction Energies, J. Chem. Theory Comput. 9, 4453 (2013) http://pubs.acs.org/doi/abs/10.1021/ct400660j -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola|,|alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------