From owner-chemistry@ccl.net Tue Mar 2 01:29:01 2010 From: "Joy Ku joyku|*|stanford.edu" To: CCL Subject: CCL: 3D RNA Modeling and Simulation Workshop Message-Id: <-41345-100302012735-16979-TiJbdoUoZ+PmcExQvaT33g _ server.ccl.net> X-Original-From: "Joy Ku" Date: Tue, 2 Mar 2010 01:27:31 -0500 Sent to CCL by: "Joy Ku" [joyku]_[stanford.edu] What: 3D RNA Modeling and Simulation Workshop When: March 29, 2010, 9am to 5pm Where: University of Illinois at Chicago Cost: Free to attend. Registration is required, though, and spaces are limited. For more information and/or to register, visit http://simbios.stanford.edu/RNAWorkshop.htm Description: The structure and dynamics of molecules is central to understanding biological function, and yet most experimentalists find existing structural modeling tools excessively limited in scope and difficult to use. In Simbios 3D RNA Modeling and Simulation Workshop, participants will learn new tools that enable them to generate structures and dynamical trajectories based on their hypotheses, limited experimental information, and/or initial coordinates. The presented freely available molecular modeling and simulation tools were designed to be easily applied by experimentalists to problems of current biological interest: 1. Nucleic Acid Simulation Tool (NAST) - Generates a large number of conformationally diverse coarse-grained 3D structures that satisfy user-provided secondary and tertiary contacts. http://simtk.org/home/nast 2. RNABuilder: Constructs structural models of RNA by enforcing user-provided base pairing interactions and other structural constraints. http://simtk.org/home/rnatoolbox 3. OpenMM Zephyr: Generates a full atomic simulation using a version of the GROMACS molecular dynamics package that can be accelerated on GPUs. http://simtk.org/home/zephyr From owner-chemistry@ccl.net Tue Mar 2 05:53:00 2010 From: "Diksha Dharmendra Makwani diksha_-_iitb.ac.in" To: CCL Subject: CCL:G: gamma calculations with G03 Message-Id: <-41346-100302054856-22774-ZI6+xytvt6Z2V+iY1jtqiQ]*[server.ccl.net> X-Original-From: "Diksha Dharmendra Makwani" Date: Tue, 2 Mar 2010 05:48:52 -0500 Sent to CCL by: "Diksha Dharmendra Makwani" [diksha^_^iitb.ac.in] Can we calculate second hyperpolarizability gamma with gaussian 03? If yes, what should be the keyword for it. Diksha Makwani Department of Physics IIT Bombay Powai Mumbai India From owner-chemistry@ccl.net Tue Mar 2 07:23:00 2010 From: "Wendy Anne Warr wendy/a\warr.com" To: CCL Subject: CCL: Report Message-Id: <-41347-100302072149-23742-2oUbksw4S4pITttNE5IrdQ[a]server.ccl.net> X-Original-From: "Wendy Anne Warr" Date: Tue, 2 Mar 2010 07:21:46 -0500 Sent to CCL by: "Wendy Anne Warr" [wendy ~~ warr.com] Report on the ACS Meeting Washington, DC, August 16-20, 2009 Includes 31 transcripts of papers on cheminformatics, federated search, and chemical text mining and public molecular databases, plus six months worth of news from 80 companies. It includes presentations from the Herman Skolnik Award Symposium honoring Yvonne Martin. Contents list etc. at http://www.warr.com. Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England +44 (0)1477 533837 wendy-.-warr.com http://www.warr.com From owner-chemistry@ccl.net Tue Mar 2 08:35:01 2010 From: "Sergio Emanuel Galembeck segalemb!=!usp.br" To: CCL Subject: CCL:G: spin contamination and geometry optimization Message-Id: <-41348-100302082807-22456-CMGcOcsWundp9yrs2HKt4g[*]server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 02 Mar 2010 09:27:52 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb.*o*.usp.br] Hello, I am doing some MP2 calculations on organic radicals and I observed a strong spin contamination. By searching in internet, I found that iop(5/14=2) instructs G03 to use the annihilated wavefunction in population analysis. Is it possible to use this iop in geometry optimizations, obtaining a geometry that corresponds to the doublet spin state? Thanks, Sergio ============================================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil phone: +55-16-3602-37-65 fax: +55-16-3602-48-38 e-mail: segalemb_at_usp.br ============================================================== From owner-chemistry@ccl.net Tue Mar 2 09:11:00 2010 From: "Wendy Anne Warr wendy|,|warr.com" To: CCL Subject: CCL: Report on ACS Meeting Message-Id: <-41349-100302071700-23385-YCv88VTjz2c3y7n2pwhYDA%a%server.ccl.net> X-Original-From: "Wendy Anne Warr" Date: Tue, 2 Mar 2010 07:16:56 -0500 Sent to CCL by: "Wendy Anne Warr" [wendy__warr.com] My report on the ACS Meeting Washington, DC, August 16-20, 2009 is a bumper issue with 31 transcripts of papers on cheminformatics, federated search, and chemical text mining and public molecular databases, plus six months worth of news from 80 companies. It includes presentations from the Herman Skolnik Award Symposium honoring Yvonne Martin. Contents list and order form at http://www.warr.com. (Note that the report itself will not be on the Web.) Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England +44 (0)1477 533837 wendy^-^warr.com http://www.warr.com From owner-chemistry@ccl.net Tue Mar 2 10:57:00 2010 From: "CompChem Group Compchemgroup1**gmail.com" To: CCL Subject: CCL:G: Scaling Factor for thermodynamic calculations Message-Id: <-41350-100302091505-31684-Pz8wOHYgfJQn7t7vbQMueA/a\server.ccl.net> X-Original-From: "CompChem Group " Date: Tue, 2 Mar 2010 09:15:00 -0500 Sent to CCL by: "CompChem Group " [Compchemgroup1%%gmail.com] Dear All, I want to use scaling factor for calculation the thermodynamic parameters for some molecular systems using B3LYP/6-311g(d,p), Gaussian 09. I found in literature the scaling factor for such model chemistry = 0.967 0.021. Because this is first time I use scaling factor. I want to ensure this method is valid or not? It is done by adding "SCALE=0.967" in the input file, right. Thanks in advance, CCG From owner-chemistry@ccl.net Tue Mar 2 11:32:00 2010 From: "=!yahoo.com" To: CCL Subject: CCL:G: G03:Different Charges on Molecules Message-Id: <-41351-100302100636-3547-uwJjxEtvE2mKvXIJ7Xrolw=server.ccl.net> X-Original-From: . yahoo.com> Content-Type: multipart/alternative; boundary="0-1672122344-1267539096=:50076" Date: Tue, 2 Mar 2010 06:11:36 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: :yahoo.com] --0-1672122344-1267539096=:50076 Content-Type: text/plain; charset=us-ascii Dear CCL subscribers, I have two molecules near each other. How can I assign different amount of charges to each molecule in Gaussian 03? Thanks in advance. Regards, AF --0-1672122344-1267539096=:50076 Content-Type: text/html; charset=us-ascii
Dear CCL subscribers,
I have two molecules near each other. How can I assign different amount of charges to each molecule in Gaussian 03?
Thanks in advance.
Regards,
AF

--0-1672122344-1267539096=:50076-- From owner-chemistry@ccl.net Tue Mar 2 12:13:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom * gmail.com" To: CCL Subject: CCL:G: G03:Different Charges on Molecules Message-Id: <-41352-100302121045-27254-iuDx584H1PjfQPE3ZDf2wA[]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: multipart/alternative; boundary=0016367fadd1d92da90480d45903 Date: Tue, 2 Mar 2010 18:03:55 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom!A!gmail.com] --0016367fadd1d92da90480d45903 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Arash, in general only one of the charge distributions is the electronic ground state, and the other is an excited state. Depending on your particular molecules, it may be that the lowest singlet and triplet states are the ones you want. You can optimize these separately by specifying the total spin of the system, or you can use a method that gives you many excited states in one go, such as CI methods or TDDFT (but beware the charge transfer problem). You then need to analyze the excited states to find out which ones correspond to the differently charged molecules. If your molecules have symmetry this will help you a lot. What are your molecules? It may be that gaussian has some other way to artificially constrain charge to a particular molecule, perhaps someone else knows about that. Sincerely, Ulf Ekstr=F6m, VU University Amsterdam. --0016367fadd1d92da90480d45903 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Arash,
in general only one of the charge distributions is the elect= ronic ground state,
and the other is an excited state. Depending on your= particular molecules,
it may be that the lowest singlet and triplet sta= tes are the ones you want.
You can optimize these separately by specifying the total spin of the
sy= stem, or you can use a method that gives you many excited states
in one = go, such as CI methods or TDDFT (but beware the
charge transfer problem= ). You then need to analyze the excited states
to find out which ones correspond to the differently charged molecules.
= If your molecules have symmetry this will help you a lot. What are your
= molecules?

It may be that gaussian has some other way to artificiall= y constrain
charge to a particular molecule, perhaps someone else knows about that.
=

Sincerely,
Ulf Ekstr=F6m, VU University Amsterdam.

--0016367fadd1d92da90480d45903-- From owner-chemistry@ccl.net Tue Mar 2 12:54:00 2010 From: "Serge Gorelsky gorelsky~!~gmail.com" To: CCL Subject: CCL:G: G03:Different Charges on Molecules Message-Id: <-41353-100302122625-9544-wlj79LMFI3trGquUo5V6aQ__server.ccl.net> X-Original-From: Serge Gorelsky Content-Type: multipart/alternative; boundary=0016e6d77e12cb33690480d49108 Date: Tue, 2 Mar 2010 12:19:33 -0500 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky ~ gmail.com] --0016e6d77e12cb33690480d49108 Content-Type: text/plain; charset=UTF-8 You can assign the different charges to different molecular parts in a single calculation by using the "fragment-defined" initial guess for the wavefunction in Gaussian 03. Please see the Appendix 2 of the AOMix manual ( www.sg-chem.net) for more details. On Tue, Mar 2, 2010 at 9:11 AM, =!yahoo.com < owner-chemistry*o*ccl.net> wrote: > Dear CCL subscribers, > I have two molecules near each other. How can I assign different amount of > charges to each molecule in Gaussian 03? > Thanks in advance. > Regards, > AF > > -- Best regards, Serge Gorelsky --0016e6d77e12cb33690480d49108 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You can assign the different charges to different=C2=A0molecular parts in a= single calculation=C2=A0by using the "fragment-defined" initial = guess for the wavefunction in Gaussian 03. Please see the Appendix 2 of the= AOMix manual (www.sg-chem.net) for= more details.

On Tue, Mar 2, 2010 at 9:11 AM, =3D!yahoo.com <owner-chemistry*o*ccl.net> wrote:




--
Best regards,
= =C2=A0Serge Gorelsky
--0016e6d77e12cb33690480d49108-- From owner-chemistry@ccl.net Tue Mar 2 14:26:01 2010 From: "Dr. Xiaofeng (Frank) Duan duanx.ctr#%#afrl.hpc.mil" To: CCL Subject: CCL: Stochastic Search for Isomers Message-Id: <-41354-100302115028-15359-NKFJHoiCwgZU4BlwAey3aw*|*server.ccl.net> X-Original-From: "Dr. Xiaofeng (Frank) Duan" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Mar 2010 11:03:05 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. Xiaofeng (Frank) Duan" [duanx.ctr_._afrl.hpc.mil] Hi all, Does anyone know any programs that have features to generate and filter out stable isomers for a set of atoms (around 8-10 atoms)? Thanks! Frank Duan -- From owner-chemistry@ccl.net Tue Mar 2 15:58:01 2010 From: "Morad El-Hendawy m80elhendawy a yahoo.com" To: CCL Subject: CCL:G: G03:Different Charges on Molecules Message-Id: <-41355-100302144215-7430-4+/iRv0VbyLDjlOTGkwqPw()server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-499904484-1267555324=:64153" Date: Tue, 2 Mar 2010 10:42:04 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy,yahoo.com] --0-499904484-1267555324=:64153 Content-Type: text/plain; charset=us-ascii Hi, Try your calculations with ONIOM (QM/QM). It may be helpful in your case. Regards, Morad --- On Tue, 3/2/10, !yahoo.com wrote: > From: yahoo.com Subject: CCL:G: G03:Different Charges on Molecules To: "El-Hendawy, Morad Metwally " Date: Tuesday, March 2, 2010, 4:11 PM Dear CCL subscribers, I have two molecules near each other. How can I assign different amount of charges to each molecule in Gaussian 03? Thanks in advance. Regards, AF --0-499904484-1267555324=:64153 Content-Type: text/html; charset=us-ascii
Dear CCL subscribers,
I have two molecules near each = other. How can I assign different amount of charges to each molecule in Gau= ssian 03?
Thanks in advance.
Regards,
AF
Hi
Try your calculations with ONIOM (QM/QM). It may be helpful in your case.
Regards,
Morad

--- On Tue, 3/2/10, !=!yahoo.com <owner-chemistry-,-ccl.net> wrote:

From: =!yahoo.com <owner-chemistry-,-ccl.net>
Subject: CCL:G: G03:Different Charges on Molecules
To: "El-Hendawy, Morad Metwally " <m80elhendawy-,-yahoo.com>
Date: Tuesday, March 2, 2010, 4:11 PM

Dear CCL subscribers,
I have two molecules near each other. How can I assign different amount of charges to each molecule in Gaussian 03?
Thanks in advance.
Regards,
AF


--0-499904484-1267555324=:64153-- From owner-chemistry@ccl.net Tue Mar 2 16:32:00 2010 From: "Morad El-Hendawy m80elhendawy^-^yahoo.com" To: CCL Subject: CCL: Stochastic Search for Isomers Message-Id: <-41356-100302160730-21521-hnIkpUqygxwW/i6XGG5qGg-x-server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-365096010-1267564038=:90862" Date: Tue, 2 Mar 2010 13:07:18 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy]^[yahoo.com] --0-365096010-1267564038=:90862 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Frank Duan, Molecular Operating Environment (MOE) program able to generate conformation= s by anyone of the following three methods: (i) Systematic search; (ii) Stochastic search; (iii) Molecular Dynamics search (This methodology is just new feature of ve= rsion 2010). All the best, Morad=20 --- On Tue, 3/2/10, Dr. Xiaofeng (Frank) Duan duanx.ctr#%#afrl.hpc.mil wrote: > From: Dr. Xiaofeng (Frank) Duan duanx.ctr#%#afrl.hpc.mil Subject: CCL: Stochastic Search for Isomers To: "El-Hendawy, Morad Metwally " Date: Tuesday, March 2, 2010, 6:03 PM Sent to CCL by: "Dr. Xiaofeng (Frank) Duan" [duanx.ctr_._afrl.hpc.mil] Hi all, Does anyone know any programs that have features to generate and filter out= stable isomers for a set of atoms (around 8-10 atoms)? Thanks! Frank Duan -- -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sh= tmlConferences: http://server.ccl.net/chemistry/a= nnouncements/conferences/=A0 =A0=A0=A0http://www.ccl.net/spammers.txt=0A=0A=0A --0-365096010-1267564038=:90862 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Frank Duan,
Molecular Operating Environ= ment (MOE) program able to generate conformations by anyone of the followin= g three methods:
(i) Systematic search;
(ii) Stochastic search;
(= iii) Molecular Dynamics search (This methodology is just new feature of ver= sion 2010).
All the best,
Morad


--- On Tue, 3/2/10, Dr= . Xiaofeng (Frank) Duan duanx.ctr#%#afrl.hpc.mil <owner-chemistry- -ccl= .net> wrote:

From: Dr. Xiaofeng = (Frank) Duan duanx.ctr#%#afrl.hpc.mil <owner-chemistry- -ccl.net>
Su= bject: CCL: Stochastic Search for Isomers
To: "El-Hendawy, Morad Metwall= y " <m80elhendawy- -yahoo.com>
Date: Tuesday, March 2, 2010,= 6:03 PM


Sent to CCL by: "Dr. Xiaofeng = (Frank) Duan" [duanx.ctr_._afrl.hpc.mil]
Hi all,

Does anyone know any pr= ograms that have features to generate and filter out stable isomers for a s= et of atoms (around 8-10 atoms)?

Thanks!

Frank Duan
--
=


-=3D This is automatically added to each message by the mailing= script =3D-
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= =0A=0A --0-365096010-1267564038=:90862-- From owner-chemistry@ccl.net Tue Mar 2 18:49:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim:compchem.net" To: CCL Subject: CCL:G: G03:Different Charges on Molecules Message-Id: <-41357-100302181928-21434-Wr3QjpSTmyOYWRzmoYcD9Q a server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d78545c1bc510480d8dd17 Date: Tue, 2 Mar 2010 22:27:08 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim++compchem.net] --0016e6d78545c1bc510480d8dd17 Content-Type: text/plain; charset=ISO-8859-1 Dear Arash I believe you got enough information about your enquiry. But, using QM/QM makes restrain on charges for your molecules during charge calculation, in other words, each molecule will have an unity charge. This trick we use it just to study molecular charge change due to bonding/non-bonding of the molecule to another one or an active site. I would recommend to use R.E.D software (related to amber), it gives you lot of options to assign charges for your system (with/without restrain, different orientation, and different conformations). Sincerely; M. Ibrahim On Tue, Mar 2, 2010 at 2:11 PM, !=!yahoo.com < owner-chemistry^_^ccl.net> wrote: > Dear CCL subscribers, > I have two molecules near each other. How can I assign different amount of > charges to each molecule in Gaussian 03? > Thanks in advance. > Regards, > AF > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim^_^compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6d78545c1bc510480d8dd17 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Arash
I believe you got enough information about your enquiry.
But, using QM/QM makes restrain on charges for your=A0molecules duri= ng charge calculation, in other words, each molecule will have an unity cha= rge. This trick we use it just to study molecular charge change due to bond= ing/non-bonding of the molecule to another one or an active site.
I would recommend to use R.E.D software (related to amber), it gives y= ou lot of options to=A0assign=A0charges for your system (with/without restr= ain, different=A0orientation, and different conformations).
Since= rely;
M. Ibrahim

On Tue, Mar 2, 2010 at 2:11 PM, =3D!yahoo.co= m <owner-chemistry^_^ccl.net> wrote:
Dear CCL s= ubscribers,
I have two molecules near each other. How can I assign different amount of = charges to each molecule in Gaussian 03?
Thanks in advance.
Regards,<= br>AF




--
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Univ= ersity of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim^_^compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 Fax No.: +20862342601
--0016e6d78545c1bc510480d8dd17--