Silicos NV is pleased = to announce the release of its open source online application tool = called ProfiLIB, built on top of the Open Babel 2.3.0 C++ library and = incorporating many of Silicos' open source programs. ProfiLIB is an = online application tool that can be accessed from the Silicos = website without any charges [http://www.silicos.com]. An example = report is also available from this website.

The = profiLIB tool generates in an automated fashion a full report of the = molecular characteristics of a user-provided compound library. The first = part of the analysis is made in terms of molecular descriptors and = physico-chemical properties. These properties are compared to Silicos' = in-house vendor compound library Simosa=99 to position the input set in = relation to an average sample of these vendor compounds. Secondly, the = library is mapped onto the vendor chemical space using Silicos' open = source Spectrophores=99. This mapping is overlaid with a set of diverse = compound classes linked to specific drug targets. In the third and final = part of the analysis, the library is characterized in terms of the = molecular scaffolds represented by the set. Two distinct scaffold sets = are statistically compared with the scaffolds from the vendor compounds = > from Simosa=99.

Silicos NV is a Belgian = service-based company providing services and tools in the fields of = chemoinformatics, chemogenomics and database characterisation. Several = other chemoinformatics tools have been brought into the open source = domain by Silicos, including SIEVE, PHARAO, PIRAMID, and OBSPECTROPHORE, = the latter being part of Open Babel 2.3.

For = more information about ProfiLIB, or any other tools or services, please = contact Silicos at info%a%silicos.com.

Kind regards,

Hans De = Winter

Silicos = NV

= --Apple-Mail-13-77840129-- From owner-chemistry@ccl.net Tue Feb 22 08:28:00 2011 From: "rocky walden rocky.walden19+*+gmail.com" To: CCL Subject: CCL: Explanation / Guidance needed.. Message-Id: <-43996-110222020321-4442-CxYxVehmUy5TIDVFajM8hQ-,-server.ccl.net> X-Original-From: rocky walden Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Feb 2011 08:03:15 +0100 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19###gmail.com] ---------- Forwarded message ---------- > From: "rocky walden rocky.walden19 _ gmail.com" Date: Thu, 10 Feb 2011 23:35:01 +0100 Subject: CCL: Explanation / Guidance needed.. To: "Walden, Rocky James " Hello All, I am new to this Computational chemistry, i am planning to do some Pratical course in Computational Chemisty focusing some MD Simulations of a Protein with a set of synthesized ligands. We have NAMD, GROMACS Suite for Calculations / simulations and have a cluster with 40 processors (Dual core). I am struck with which type of simulation should i do Either Picosecond or FemtoSecond or Nanosecond simulation. What are the different types of simulations available based on time scale (pico/femto/nano/ Micro). What should be the size of steps ( what happens when i use more no of steps / or i decrease the no of steps). Thanks walden.R From owner-chemistry@ccl.net Tue Feb 22 09:02:00 2011 From: "Mikael Johansson mikael.johansson||iki.fi" To: CCL Subject: CCL: Explanation / Guidance needed.. Message-Id: <-43997-110222085455-18461-n8wt7cEuNgfDMtna2vqdeQ*o*server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 22 Feb 2011 15:54:45 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson|iki.fi] Hello walden.R, You questions are much too vague and basic, you need to display at least some sort of effort of figuring things out yourself. Start here: http://en.wikipedia.org/wiki/Molecular_dynamics Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ On Tue, 22 Feb 2011, rocky walden rocky.walden19+*+gmail.com wrote: > I am new to this Computational chemistry, i am planning to do some > Pratical course in Computational Chemisty focusing some MD Simulations of a > Protein with a set of synthesized ligands. > We have NAMD, GROMACS Suite for Calculations / simulations and have a > cluster with 40 processors (Dual core). > > I am struck with which type of simulation should i do Either Picosecond > or FemtoSecond or Nanosecond simulation. > What are the different types of simulations available based on time > scale (pico/femto/nano/ Micro). > What should be the size of steps ( what happens when i use more no of > steps / or i decrease the no of steps). > > > > Thanks > walden.R> > From owner-chemistry@ccl.net Tue Feb 22 10:51:01 2011 From: "Arindam Ganguly arindamganguly : gmail.com" To: CCL Subject: CCL: Explanation / Guidance needed.. Message-Id: <-43998-110222101045-24279-RyhGKDb5O7QGC/0mkpNvdw[*]server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=0016367b60fac936af049ce06127 Date: Tue, 22 Feb 2011 10:10:33 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly+*+gmail.com] --0016367b60fac936af049ce06127 Content-Type: text/plain; charset=ISO-8859-1 Hello Walden, I agree with Mikael, you're asking some very basic questions. My personal recommendation would be to read this book. It has very good introductions to basic concepts into MD. http://www.amazon.com/Understanding-Molecular-Simulation-Second-Computational/dp/0122673514/ref=sr_1_4?s=books&ie=UTF8&qid=1298386166&sr=1-4 Arindam On Tue, Feb 22, 2011 at 8:54 AM, Mikael Johansson mikael.johansson||iki.fi < owner-chemistry()ccl.net> wrote: > > Sent to CCL by: Mikael Johansson [mikael.johansson|iki.fi] > > Hello walden.R, > > You questions are much too vague and basic, you need to display at least > some sort of effort of figuring things out yourself. Start here: > http://en.wikipedia.org/wiki/Molecular_dynamics > > Have a nice day, > Mikael J. > http://www.iki.fi/~mpjohans/ > > > > On Tue, 22 Feb 2011, rocky walden rocky.walden19+*+gmail.com wrote: > > I am new to this Computational chemistry, i am planning to do some >> Pratical course in Computational Chemisty focusing some MD Simulations of >> a >> Protein with a set of synthesized ligands. >> We have NAMD, GROMACS Suite for Calculations / simulations and have a >> cluster with 40 processors (Dual core). >> >> I am struck with which type of simulation should i do Either Picosecond >> or FemtoSecond or Nanosecond simulation. >> What are the different types of simulations available based on time >> scale (pico/femto/nano/ Micro). >> What should be the size of steps ( what happens when i use more no of >> steps / or i decrease the no of steps). >> >> >> >> Thanks >> walden.Rhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Arindam Ganguly, Ph.D. Postdoctoral Researcher University of Michigan, Ann Arbor Dept. of Chemistry, 930 N. University Avenue, Ann Arbor, MI-48109-1055, USA Phone:-816-419-1806 Email:- ArindamGanguly()gmail.com http://www.linkedin.com/in/arindamganguly --0016367b60fac936af049ce06127 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello Walden,
I agree with Mikael, you're asking some very basic que= stions. My personal recommendation would be to read this book.=A0 It has ve= ry good introductions to basic concepts into MD. h= ttp://www.amazon.com/Understanding-Molecular-Simulation-Second-Computationa= l/dp/0122673514/ref=3Dsr_1_4?s=3Dbooks&ie=3DUTF8&qid=3D1298386166&a= mp;sr=3D1-4

Arindam

On Tue, Feb 22, 2011 at 8:54 = AM, Mikael Johansson mikael.johansson||iki.fi= <owner-che= mistry()ccl.net> wrote:

Sent to CCL by: Mikael Johansson [mikael.johansson|iki.fi]

Hello walden.R,

You questions are much too vague and basic, you need to display at least so= me sort of effort of figuring things out yourself. Start here:
=A0http://en.wikipedia.org/wiki/Molecular_dynamics

Have a nice day,
=A0 =A0Mikael J.
=A0 =A0http:/= /www.iki.fi/~mpjohans/

On Tue, 22 Feb 2011, rocky walden rocky.walden19+*+gmail.com wrote:

=A0 =A0 I am new to this Computational chemistry, i am planning to do some=
Pratical course in Computational Chemisty focusing some MD Simulations of a=
Protein with a set of synthesized ligands.
=A0 =A0 We have NAMD, GROMACS =A0Suite for Calculations / simulations and = have a
cluster with 40 processors (Dual core).

=A0 =A0I am struck with which type of simulation should i do Either Picose= cond
or FemtoSecond =A0or Nanosecond simulation.
=A0 =A0What are the different types of simulations available based on time=
scale (pico/femto/nano/ Micro).
=A0 What should be the size of steps ( what happens when i use more no of<= br> steps / or i decrease the no of steps).

Thanks
walden.R>

-=3D This is automatically added to each message by the mailing script =3D-=
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--
Arindam Gan= guly, Ph.D.
Postdoctoral Researcher
University of Michigan, Ann Arbor=
Dept. of Chemistry,
930 N. University Avenue,
Ann Arbor, MI-48109= -1055, USA
Phone:-816-419-1806
Email:- ArindamGanguly()gmail.com
http://www.linkedin.com/in/a= rindamganguly
--0016367b60fac936af049ce06127-- From owner-chemistry@ccl.net Tue Feb 22 13:49:01 2011 From: "may abdelghani may01dz^yahoo.fr" To: CCL Subject: CCL: AOMix-CDA charge decomposition analysis Message-Id: <-43999-110222134252-32428-oGuO15V1E9bplrR8YGqk2Q++server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1592987945-1298400164=:81167" Date: Tue, 22 Feb 2011 18:42:44 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz**yahoo.fr] --0-1592987945-1298400164=:81167 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable =0A=0ADear CCl'ers,=0A=0ABellow is my AOMix-CDA results:=0A=0AIs it normal = to see a minus sign before the value of the donation/back-donation=0A v= alues?It is normal to get a value of 1.273 for the donation from=0A fra= g1 to fragm2=E2=80=A6I think that it should not be greater than 1?Alpha-spi= n MO=C2=A0=C2=A0=C2=A0 1->2=C2=A0=C2=A0 2->1=20 =C2=A0HOMO -77 (# 52)=C2=A0 0.000=C2=A0 0.004=20 =C2=A0HOMO -76 (# 53)=C2=A0 0.000=C2=A0 0.002=20 =C2=A0HOMO -69 (# 60)=C2=A0 0.000=C2=A0 0.005=20 =C2=A0HOMO -68 (# 61)=C2=A0 0.000 -0.001=20 =C2=A0HOMO -67 (# 62)=C2=A0 0.000=C2=A0 0.001=20 =C2=A0HOMO -65 (# 64)=C2=A0 0.000=C2=A0 0.003=20 =C2=A0HOMO -64 (# 65)=C2=A0 0.000=C2=A0 0.005=20 =C2=A0HOMO -54 (# 75)=C2=A0 0.000 -0.001=20 =C2=A0HOMO -53 (# 76)=C2=A0 0.001 -0.004=20 =C2=A0HOMO -50 (# 79)=C2=A0 0.000 -0.004=20 =C2=A0HOMO -49 (# 80)=C2=A0 0.002=C2=A0 0.014=20 =C2=A0HOMO -48 (# 81) -0.004=C2=A0 0.016=20 =C2=A0HOMO -47 (# 82)=C2=A0 0.001 -0.004=20 =C2=A0HOMO -42 (# 87) -0.003 -0.003=20 =C2=A0HOMO -41 (# 88)=C2=A0 0.001 -0.005=20 =C2=A0HOMO -39 (# 90)=C2=A0 0.000=C2=A0 0.006=20 =C2=A0HOMO -38 (# 91) -0.001 -0.003=20 =C2=A0HOMO -37 (# 92)=C2=A0 0.000 -0.006=20 =C2=A0HOMO -36 (# 93)=C2=A0 0.033 -0.029=20 =C2=A0HOMO -35 (# 94)=C2=A0 0.016 -0.043=20 =C2=A0HOMO -34 (# 95) -0.001 -0.006=20 =C2=A0HOMO -33 (# 96)=C2=A0 0.002 -0.003=20 =C2=A0HOMO -32 (# 97)=C2=A0 0.009 -0.003=20 =C2=A0HOMO -31 (# 98)=C2=A0 0.000 -0.003=20 =C2=A0HOMO -30 (# 99)=C2=A0 0.000 -0.002=20 =C2=A0HOMO -29 (#100)=C2=A0 0.000=C2=A0 0.002=20 =C2=A0HOMO -26 (#103) -0.001 -0.004=20 =C2=A0HOMO -25 (#104)=C2=A0 0.000 -0.001=20 =C2=A0HOMO -17 (#112)=C2=A0 0.001 -0.003=20 =C2=A0HOMO -16 (#113)=C2=A0 0.001=C2=A0 0.003=20 =C2=A0HOMO -15 (#114)=C2=A0 0.000=C2=A0 0.004=20 =C2=A0HOMO -12 (#117)=C2=A0 0.225=C2=A0 0.067=20 =C2=A0HOMO -11 (#118)=C2=A0 0.183=C2=A0 0.045=20 =C2=A0HOMO -10 (#119)=C2=A0 0.005 -0.006=20 =C2=A0HOMO=C2=A0 -9 (#120)=C2=A0 0.002 -0.005=20 =C2=A0HOMO=C2=A0 -8 (#121)=C2=A0 0.000=C2=A0 0.020=20 =C2=A0HOMO=C2=A0 -7 (#122)=C2=A0 0.005=C2=A0 0.015=20 =C2=A0HOMO=C2=A0 -6 (#123)=C2=A0 0.014=C2=A0 0.011=20 =C2=A0HOMO=C2=A0 -5 (#124)=C2=A0 0.011=C2=A0 0.004=20 =C2=A0HOMO=C2=A0 -4 (#125)=C2=A0 0.000=C2=A0 0.004=20 =C2=A0HOMO=C2=A0 -3 (#126)=C2=A0 0.002=C2=A0 0.007=20 =C2=A0HOMO=C2=A0 -2 (#127)=C2=A0 0.078=C2=A0 0.032=20 =C2=A0HOMO=C2=A0 -1 (#128)=C2=A0 0.059=C2=A0 0.022=20 =C2=A0HOMO=C2=A0=C2=A0 0 (#129) -0.001 -0.055=20 =C2=A0-----------------------------=20 =C2=A0Total over OMOs=C2=A0 0.637=C2=A0 0.097 =C2=A0=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=20 =C2=A0TotalALPHA+BETA=C2=A0 1.273=C2=A0 0.194 =0A=0A=C2=A0=0A=0A may abdelghani=09Laboratoire de chimie des mat=C3=A9riaux et des vivants: A= ctivit=C3=A9, R=C3=A9activit=C3=A9 =0A=0A=0A=0A=0A --0-1592987945-1298400164=:81167 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A=0A=0A=0A=0A --0-1592987945-1298400164=:81167-- From owner-chemistry@ccl.net Tue Feb 22 15:04:00 2011 From: "Serge Gorelsky gorelsky/a\gmail.com" To: CCL Subject: CCL: AOMix-CDA charge decomposition analysis Message-Id: <-44000-110222145910-10070-Uq6U71TQ7s1C2yq6qseqzg*server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 22 Feb 2011 14:56:35 -0500 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky]^[gmail.com] On Tue, Feb 22, 2011 at 1:42 PM, may abdelghani may01dz^yahoo.fr wrote: > > Dear CCl'ers, > > Bellow is my AOMix-CDA results: > > Is it normal to see a minus sign before the value of the donation/back-donation values? negative values for donation/back-donation carry no physical value. Fortunately for your calculation, all negative values are very small in magnitude and can be assumed to be zeros. > > It is normal to get a value of 1.273 for the donation from frag1 to fragm2…I think that it should not be greater than 1? the TOTAL donation values for multi-electron / multi-orbital systems can certainly be greater than 1 because they include MANY orbital interactions, not just one pair of orbitals. > Alpha-spin MO 1->2 2->1 > HOMO -77 (# 52) 0.000 0.004 > HOMO -76 (# 53) 0.000 0.002 > HOMO -69 (# 60) 0.000 0.005 > HOMO -68 (# 61) 0.000 -0.001 > HOMO -67 (# 62) 0.000 0.001 > HOMO -65 (# 64) 0.000 0.003 > HOMO -64 (# 65) 0.000 0.005 > HOMO -54 (# 75) 0.000 -0.001 > HOMO -53 (# 76) 0.001 -0.004 > HOMO -50 (# 79) 0.000 -0.004 > HOMO -49 (# 80) 0.002 0.014 > HOMO -48 (# 81) -0.004 0.016 > HOMO -47 (# 82) 0.001 -0.004 > HOMO -42 (# 87) -0.003 -0.003 > HOMO -41 (# 88) 0.001 -0.005 > HOMO -39 (# 90) 0.000 0.006 > HOMO -38 (# 91) -0.001 -0.003 > HOMO -37 (# 92) 0.000 -0.006 > HOMO -36 (# 93) 0.033 -0.029 > HOMO -35 (# 94) 0.016 -0.043 > HOMO -34 (# 95) -0.001 -0.006 > HOMO -33 (# 96) 0.002 -0.003 > HOMO -32 (# 97) 0.009 -0.003 > HOMO -31 (# 98) 0.000 -0.003 > HOMO -30 (# 99) 0.000 -0.002 > HOMO -29 (#100) 0.000 0.002 > HOMO -26 (#103) -0.001 -0.004 > HOMO -25 (#104) 0.000 -0.001 > HOMO -17 (#112) 0.001 -0.003 > HOMO -16 (#113) 0.001 0.003 > HOMO -15 (#114) 0.000 0.004 > HOMO -12 (#117) 0.225 0.067 > HOMO -11 (#118) 0.183 0.045 > HOMO -10 (#119) 0.005 -0.006 > HOMO -9 (#120) 0.002 -0.005 > HOMO -8 (#121) 0.000 0.020 > HOMO -7 (#122) 0.005 0.015 > HOMO -6 (#123) 0.014 0.011 > HOMO -5 (#124) 0.011 0.004 > HOMO -4 (#125) 0.000 0.004 > HOMO -3 (#126) 0.002 0.007 > HOMO -2 (#127) 0.078 0.032 > HOMO -1 (#128) 0.059 0.022 > HOMO 0 (#129) -0.001 -0.055 > ----------------------------- > Total over OMOs 0.637 0.097 > ============================= > TotalALPHA+BETA 1.273 0.194 > > > > > > > > > > > > may abdelghani > Laboratoire de chimie des matériaux et des vivants: Activité, Réactivité > -- Best regards, Serge Gorelsky From owner-chemistry@ccl.net Tue Feb 22 15:38:00 2011 From: "Iain Moal Iain.Moal^_^cancer.org.uk" To: CCL Subject: CCL: Explanation / Guidance needed.. Message-Id: <-44001-110222095826-24669-dHmwRYXgpnJ+DR9Nhz6A6A]|[server.ccl.net> X-Original-From: Iain Moal Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Feb 2011 14:57:39 +0000 MIME-Version: 1.0 Sent to CCL by: Iain Moal [Iain.Moal..cancer.org.uk] The length of the simulation depends on the timescale of the phenomenon you are looking at. If you want to calculate binding affinity from a high-resolution protein-ligand crystal structure using MM-PBSA, two nanoseconds should suffice (you can split this up into multuple runs starting with different random number seeds), plus, of course, minimisation, heating up and equillibration (possibly two steps of equillibration, one with weak restrains and one without restrains). As for the timestep, 1fs is usual, although you can increase this to 2fs if you use 'shake', which keeps covalent bonds to hydrogen fixed - as the H-X bonds ocillate with the highest frequency. If you decrease the timestep, you'll still get good results, only the calculation becomes computationally expensive. If you set the timestep too high, atoms will crash into each other, feel huge repulsion forces and leave you with a worthless trajectory. There are a number of good MD tutorials on the internet, which should get you familiarised with the basic steps in setting up an MD simulation. After that, plenty of papers use MD to study protein-ligand interactions, so consult them, identify any idiosyncrasies in your stucture (eg, using homology models, or docked ligands instead of a crystal structure of the complex etx...), and following the consensus should leave you with a decent trajectory. Iain Moal ________________________________________ > From: owner-chemistry+iain.moal==cancer.org.uk#,#ccl.net [owner-chemistry+iain.moal==cancer.org.uk#,#ccl.net] On Behalf Of rocky walden rocky.walden19+*+gmail.com [owner-chemistry#,#ccl.net] Sent: 22 February 2011 07:03 To: Iain Moal Subject: CCL: Explanation / Guidance needed.. Sent to CCL by: rocky walden [rocky.walden19###gmail.com] ---------- Forwarded message ---------- > From: "rocky walden rocky.walden19 _ gmail.com" Date: Thu, 10 Feb 2011 23:35:01 +0100 Subject: CCL: Explanation / Guidance needed.. To: "Walden, Rocky James " Hello All, I am new to this Computational chemistry, i am planning to do some Pratical course in Computational Chemisty focusing some MD Simulations of a Protein with a set of synthesized ligands. We have NAMD, GROMACS Suite for Calculations / simulations and have a cluster with 40 processors (Dual core). I am struck with which type of simulation should i do Either Picosecond or FemtoSecond or Nanosecond simulation. What are the different types of simulations available based on time scale (pico/femto/nano/ Micro). What should be the size of steps ( what happens when i use more no of steps / or i decrease the no of steps). Thanks walden.Rhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From owner-chemistry@ccl.net Tue Feb 22 16:13:00 2011 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas],[chem.elte.hu" To: CCL Subject: CCL:G: Optimization error Message-Id: <-44002-110222155517-32172-c331/zhk+nsGkSbPBG3FqQ[A]server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Tue, 22 Feb 2011 21:54:39 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas^chem.elte.hu] Dear Ehsan, Please, send me the output or at least the last few hundred lines. If it is really an optimization related problem I might be able to help you. Best wishes, �d�n Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry E�tv�s Lor�nd University, Budapest 1/A P�zm�ny P�ter s�t�ny H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Tuesday 22 February 2011 13:14:22 Ehsan Shakerzadeh ehsan_shakerzadeh-*-yahoo.com wrote: > Sent to CCL by: "Ehsan Shakerzadeh" [ehsan_shakerzadeh() yahoo.com] > Dear All, > I want to optimize a structure which it contains 10 Selenium (Se) atoms > with MNDO method using G98W. After some minute it is failed with an error. > What can I do? Thanks in advance

=0A=0A

Dear CCl'ers,

=0A=0A

Bellow is my AOMix-CDA results:

=0A=0A<= ol style=3D"margin-top: 0cm;" start=3D"1" type=3D"1">

Is it<= /span> normal to <= /span>see a minus sign before the value of the donation/back-donation=0A values?

It is normal to get a value of 1.273 for the = donation from=0A frag1 to fragm2=E2=80=A6I think that it should not<= span style=3D"" lang=3D"EN"> be greater than 1?=

Alpha-spin MO 1->2 = 2->1
HOMO -77 (# 52) 0.000 0.004
HOMO -= 76 (# 53) 0.000 0.002
HOMO -69 (# 60) 0.000&nbs= p; 0.005
HOMO -68 (# 61) 0.000 -0.001
HOMO -67 (# 62) 0.000 0.001
HOMO -65 (# 64) 0.000&n= bsp; 0.003
HOMO -64 (# 65) 0.000 0.005
HOMO= -54 (# 75) 0.000 -0.001
HOMO -53 (# 76) 0.001 -0.004=
HOMO -50 (# 79) 0.000 -0.004
HOMO -49 (# 80)&nbs= p; 0.002 0.014
HOMO -48 (# 81) -0.004 0.016
= ;HOMO -47 (# 82) 0.001 -0.004
HOMO -42 (# 87) -0.003 -0.003=
HOMO -41 (# 88) 0.001 -0.005
HOMO -39 (# 90)&nbs= p; 0.000 0.006
HOMO -38 (# 91) -0.001 -0.003
HOMO= -37 (# 92) 0.000 -0.006
HOMO -36 (# 93) 0.033 -0.029=
HOMO -35 (# 94) 0.016 -0.043
HOMO -34 (# 95) -0.= 001 -0.006
HOMO -33 (# 96) 0.002 -0.003
HOMO -32 = (# 97) 0.009 -0.003
HOMO -31 (# 98) 0.000 -0.003
= HOMO -30 (# 99) 0.000 -0.002
HOMO -29 (#100) 0.000 0.002
HOMO -26 (#103) -0.001 -0.004 HOMO -25 (#104) 0.000 -0.001
HOMO -17 (#112) 0= .001 -0.003
HOMO = -16 (#113) 0.001 0.003
HOMO -15 (#114) 0.000&nb= sp; 0.004
HOMO -12 (#117) 0.225 0.067
HOMO = -11 (#118) 0.183 0.045
HOMO -10 (#119) 0.005 -0= .006
HOMO -9 (#120)= 0.002 -0.005
HOMO -8 (#121) 0.000 = 0.020
HOMO -7 (#122) 0.005 0.015
HOM= O -6 (#123) 0.014 0.011
HOMO -5 (#124)&nb= sp; 0.011 0.004
HOMO -4 (#125) 0.000 0.00= 4
HOMO -3 (#126) 0.002 0.007
HOMO&nbs= p; -2 (#127) 0.078 0.032
HOMO -1 (#128) 0.059 0.022
HOMO 0 (#129) -0.001 -0.055
-----------= ------------------
Total over OMOs 0.637 0.097
&nb= sp;=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
TotalALPHA+BETA 1.273 0.194
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=0A=0A

may abdelghani=09

Laboratoire de chimie des mat=C3=A9riaux et des vi= vants: Activit=C3=A9, R=C3=A9activit=C3=A9

=0A=0A