From owner-chemistry@ccl.net Fri Mar 28 06:00:00 2008 From: "Ru Jin lilichemistry^yahoo.com" To: CCL Subject: CCL:G: Too large density matrix to intepret Message-Id: <-36567-080328055620-8533-oiVVbgUq5mRy/5YzCcHa4g#%#server.ccl.net> X-Original-From: "Ru Jin" Date: Fri, 28 Mar 2008 05:56:15 -0400 Sent to CCL by: "Ru Jin" [lilichemistry[#]yahoo.com] Hi, everyone: I am using Gauusian program G03 doing a single point calculation for C7N( seven carbon atoms and a nytrogen atiom lying on a line) at hf/6-31++g**. The resultant file gives too large value of density matrix on 4s orbital of the carbon atom neighboring the nytrogen atom, ca. 4.7 for alpha and beta respectively, and consequently 17.9 for the condensed number on this carbon atom, which is too large considering that there are only seven electrons around the neutral nytrogen atom. Who could be kindly to show me some principles about resonable value of density matrix, or more general resonable value of basis cofficient among a molecular orbital? Thanks in advance, Ru Jin From owner-chemistry@ccl.net Fri Mar 28 08:13:00 2008 From: "Michel PETITJEAN michel.petitjean:_:cea.fr" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36568-080327093940-14403-Dg3LNOHK+IFLRCrSp3G7HQ(!)server.ccl.net> X-Original-From: "Michel PETITJEAN" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C89007.93626777" Date: Thu, 27 Mar 2008 13:37:15 +0100 MIME-Version: 1.0 Sent to CCL by: "Michel PETITJEAN" [michel.petitjean~!~cea.fr] This is a multi-part message in MIME format. ------_=_NextPart_001_01C89007.93626777 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Please look at the freeware CSR: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR Best regards, Michel Petitjean. ________________________________ > From: JunJun Liu ljjlp03]~[gmail.com [mailto:owner-chemistry,+,ccl.net] Sent: Wed 3/26/2008 11:02 PM To: Michel PETITJEAN Subject: CCL: similarity of different molecules Sent to CCL by: "JunJun Liu" [ljjlp03\a/gmail.com] Hello everybody, I want to know how similar two different molecules are. Does anybody = know=20 how to do this? Any suggestions regarding algorithms or softwares are=20 highly appreciated! Thanks in advance! Junjun -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt------_=_NextPart_001_01C89007.93626777-- From owner-chemistry@ccl.net Fri Mar 28 09:00:01 2008 From: "James G Prudhomme jprudhomme * healthtech.com" To: CCL Subject: CCL: Structure-Based Design Conference - Register by April 4 Message-Id: <-36569-080328085537-8968-W2OYbZhCPGGDsppjaLWivg__server.ccl.net> X-Original-From: "James G Prudhomme" Date: Fri, 28 Mar 2008 08:55:32 -0400 Sent to CCL by: "James G Prudhomme" [jprudhomme*|*healthtech.com] *CONFERENCE EARLY BIRD DISCOUNT DEADLINE IS APRIL 4* CHI's Structure-Based Drug Design June 25-27, 2008 World Trade Center, Boston, MA www.healthtech.com/sbd/overview.aspx Those who would like to attend CHI's Structure-Based Design conference at the lowest fee are encouraged to register by Friday, April 4. Featured Case Studies: *Recent Progress in Computational Protein Design: Designing Combinatorial Protein Libraries Stephen Mayo, Ph.D., Professor of Biology and Chemistry, California Institute of Technology * The Design and Synthesis of Novel Second Generation HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) Thomas J. Tucker, Ph.D., Senior Research Fellow, Dept. of Medicinal Chemistry, Merck Research Laboratories * Structure-Based Design of HIV-1 Reverse Transcriptase Inhibitors Christopher Phillips, Ph.D., Senior Principal Scientist, Exploratory MedicinalSciences, Pfizer Global Research and Development * From Virtual Screening to Clinic: Discovery to Cevoglitazar T.R. Vedananda, Ph.D., Program Head, Diabetes & Metabolism, Novartis * The Discovery of OSI-906: A Novel, Potent, Orally Bioavailable Imidazopyrazine derived Insulin-like Growth Factor- I Receptor (IGF-1R) Inhibitor with Antitumor Activity Mark Mulvihill, Ph.D., Associate Director of Chemistry, Oncology, OSI Pharmaceuticals Lear more and register at www.healthtech.com/sbd/overview.aspx or call CHI at +1 781-972-5400. Conference registration rates increase after April 4. Regards, Jim Prudhomme Cambridge Healthtech Institute From owner-chemistry@ccl.net Fri Mar 28 09:34:01 2008 From: "sathees kannan satheeskannan * gmail.com" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36570-080328072508-11580-0DlqCL3CwjWzN888pzCA4Q|-|server.ccl.net> X-Original-From: "sathees kannan" Date: Fri, 28 Mar 2008 07:25:04 -0400 Sent to CCL by: "sathees kannan" [satheeskannan:-:gmail.com] Dear Colleagues I am using Gaussian program. I am trying to find Transition State using QST2. My system is protonated butane + iso-butane ---> butane + protonated iso-butane I have drawn structure of two reactants joined by a dummy atom(using MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to do Geometry Optimization for this structure with HF/6-21G*, Charge=1, and Spin Multiplicity=2, the calculation has been terminated with the following error, "The combination of Multiplicity 2 and 66 electrons are impossible" The fault is with multiplicity. I am not able to resolve this. Does anybody tell me how to find Charge and Multiplicity ingeneral and charge and multiplicity for the above system.? Thanks in advance SatheesKannan M.Tech(Chemical Engineering) Indian Institute of Technology - Kanpur(India) email id: satheeskannan{=}gmail.com From owner-chemistry@ccl.net Fri Mar 28 10:10:01 2008 From: "Andrew Turner andrew.turner^^ed.ac.uk" To: CCL Subject: CCL: Need your help about " RESTARTED DUE TO LINMIN FAILURE ". Message-Id: <-36571-080328052340-5030-VNC8NBRcYCNG1/5h8oTS9w..server.ccl.net> X-Original-From: Andrew Turner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Mar 2008 09:23:45 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew Turner [andrew.turner**ed.ac.uk] Hongqing, I think we need some more detail here to be able to help. What sort of system are you studying? Most often minimization problems are caused by a bad starting structure. What sort of configuration are you using? Can you check for bad contacts? Your electrostatic energy is getting out of control which is also suggestive of a bad starting configuration. You could try restraining the ions and letting the water relax first before minimizing the whole system. Andy Hongqing He leohhqa/sohu.com wrote: > Sent to CCL by: "Hongqing He" [leohhq~!~sohu.com] > Dear colleagues, > > There is an error in "Minimising the structure". > > Here is the input file: > intial minimisation solvent + ions > &cntrl > imin = 1, > maxcyc = 1000, > ncyc = 500, > ntb = 1, > cut = 10 > / > Here is a part of the output file: > > NSTEP ENERGY RMS GMAX NAME NUMBER > 1 8.2637E+11 1.0194E+11 2.6974E+13 O 26108 > > BOND = 45960.0689 ANGLE = 1519.6372 DIHED = 3968.5744 > VDWAALS = ************* EEL = -188894.8931 HBOND = 0.0000 > 1-4 VDW = 2165.8427 1-4 EEL = 19481.8190 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 50 -4.8729E+04 1.5562E+02 3.0359E+04 O 45560 > > BOND = 44692.2739 ANGLE = 1763.6515 DIHED = 3988.5936 > VDWAALS = 71542.7480 EEL = -192261.8813 HBOND = 0.0000 > 1-4 VDW = 2126.4422 1-4 EEL = 19419.0077 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 100 -8.9496E+06 2.3719E+09 5.8696E+11 O 7118 > > BOND = 39871.3056 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6536 EEL = -9078085.4300 HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 150 -1.2010E+07 4.2881E+09 1.0612E+12 O 7118 > > BOND = 39871.3077 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6553 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 200 -7.7833E+07 1.8184E+11 4.4999E+13 H2 44119 > > BOND = 39871.3142 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6611 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 250 -1.4221E+07 6.0226E+09 1.4904E+12 O 7118 > > BOND = 39871.3085 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6561 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 300 -5.3996E+07 8.7448E+10 2.1640E+13 H2 44119 > > BOND = 39871.3146 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6615 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 350 -7.2116E+06 1.5344E+09 3.7971E+11 H2 44119 > > BOND = 39871.3227 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6687 EEL = -7340037.9689 HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 400 -2.0690E+07 1.2787E+10 3.1644E+12 H2 44119 > > BOND = 39871.3166 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6633 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 450 -8.1457E+07 1.9918E+11 4.9291E+13 O 7118 > > BOND = 39871.3125 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6596 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 500 -3.0695E+07 2.8206E+10 6.9800E+12 H2 44119 > > BOND = 39871.3155 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6623 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > .... RESTARTED DUE TO LINMIN FAILURE ... > > Does anybody tell me how to solve it? > > Thanks a lot. > > Hongqing> > > -- ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner%ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Fri Mar 28 10:44:00 2008 From: "sathees kannan satheeskannan(_)gmail.com" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36572-080328092338-27038-LyfSOwUtV2vChj9+FXN97g###server.ccl.net> X-Original-From: "sathees kannan" Content-Type: multipart/alternative; boundary="----=_Part_23364_17026298.1206703869292" Date: Fri, 28 Mar 2008 17:01:09 +0530 MIME-Version: 1.0 Sent to CCL by: "sathees kannan" [satheeskannan:_:gmail.com] ------=_Part_23364_17026298.1206703869292 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Colleagues I am using Gaussian program. I am trying to find Transition State using QST2. My system is protonated butane + iso-butane ---> butane + protonated iso-butane I have drawn structure of two reactants joined by a dummy atom(using MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to do Geometry Optimization for this structure with HF/6-21G*, Charge=1, and Spin Multiplicity=2, the calculation has been terminated with the following error, "The combination of Multiplicity 2 and 66 electrons are impossible" The fault is with multiplicity. I am not able to resolve this. Does anybody tell me how to find Charge and Multiplicity ingeneral and charge and multiplicity for the above system.? Thanks in advance SatheesKannan M.Tech(Chemical Engineering) Indian Institute of Technology - Kanpur(India) email id: satheeskannan_-_gmail.com ------=_Part_23364_17026298.1206703869292 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Colleagues
I am using Gaussian program. I am trying to find Transition State using QST2.
My system is
protonated butane + iso-butane ---> butane + protonated iso-butane
I have drawn structure of two reactants joined by a dummy atom(using MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to do Geometry Optimization for this structure with HF/6-21G*, Charge=1, and Spin Multiplicity=2,
the calculation has been terminated with the following error,
"The combination of Multiplicity 2 and 66 electrons are impossible"
The fault is with multiplicity. I am not able to resolve this.

Does anybody tell me how to find Charge and Multiplicity ingeneral and charge and multiplicity for the above system.?

Thanks in advance

SatheesKannan
M.Tech(Chemical Engineering)
Indian Institute of Technology - Kanpur(India)
email id: satheeskannan_-_gmail.com ------=_Part_23364_17026298.1206703869292-- From owner-chemistry@ccl.net Fri Mar 28 11:19:01 2008 From: "Debellis Anthony CE US anthony.debellis _ ciba.com" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36573-080328105106-25121-VDZzTojmaUSjWlO/7lle6A*_*server.ccl.net> X-Original-From: Debellis Anthony CE US Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Mar 2008 10:21:07 -0400 MIME-Version: 1.0 Sent to CCL by: Debellis Anthony CE US [anthony.debellis-,-ciba.com] SatheesKannan, The multiplicity of your system is 1. There are no unpaired electrons in the system you describe. Anthony DeBellis Ciba=20 -----Original Message----- > From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net]=20 Sent: Friday, March 28, 2008 7:25 AM To: Debellis Anthony CE US Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Sent to CCL by: "sathees kannan" [satheeskannan:-:gmail.com] Dear Colleagues I am using Gaussian program. I am trying to find Transition State using QST2. My system is protonated butane + iso-butane ---> butane + protonated iso-butane I have drawn structure of two reactants joined by a dummy atom(using MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to do Geometry Optimization for this structure with HF/6-21G*, = Charge=3D1, and Spin Multiplicity=3D2, the calculation has been terminated with the following error, "The combination of Multiplicity 2 and 66 electrons are impossible" The fault is with multiplicity. I am not able to resolve this.=20 Does anybody tell me how to find Charge and Multiplicity ingeneral and charge and multiplicity for the above system.? Thanks in advance SatheesKannan M.Tech(Chemical Engineering) Indian Institute of Technology - Kanpur(India) email id: satheeskannan|*|gmail.com -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Mar 28 12:45:01 2008 From: "ramachandran chelat rcchelat^rediffmail.com" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36574-080328123303-23179-/jnGhlt/9Yox/Zi1nxF3Mw .. server.ccl.net> X-Original-From: "ramachandran chelat" Content-type: multipart/alternative; boundary="Next_1206718491---0-202.137.234.213-5359" Date: 28 Mar 2008 15:34:51 -0000 MIME-Version: 1.0 Sent to CCL by: "ramachandran chelat" [rcchelat/./rediffmail.com] This is a multipart mime message --Next_1206718491---0-202.137.234.213-5359 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear SatheesKannan,=0A=0AH^+ has no electron=0ASo multiplicity should be= 1=0A=0Amore over,=0A=0AI am sure that you missed some hydrogen atoms while= sketching the molecules.=0A=0AButane CH3-CH2-CH2-CH3 =0Aisobutane CH= (CH3)3=0Aprotonation H+=0A=0A------------------------------=0A [C= 8H21]+ =0A=0Atotal number of electrons =3D 68 electrons (your output say= s 66 !!!!!)=0A=0A=0AI am curious to know that where your proton is attachin= g with the reactant and the product system (after the job finish :)- )=0A= =0A=0Ado you mean the simple reaction=0A=0A[CH3-CH2-CH2-CH2^+] + CH(CH3)3 -= ----> CH3-CH2-CH2-CH3 & (CH3)C^+ ?=0A=0AThat can have 66 electrons=0A=0AW= hatever be the case,=0Aaddition of proton (protonation) or removal of proto= n (deprotonation), multiplicity should be 1=0A=0A=0ARamachandran,=0A=0A=0A= =0AOn Fri, 28 Mar 2008 sathees kannan satheeskannan(_)gmail.com wrote :=0A>= Dear Colleagues=0A>I am using Gaussian program. I am trying to find Transit= ion State using=0A>QST2.=0A>My system is=0A>protonated butane + iso-butane = ---> butane + protonated iso-butane=0A>I have drawn structure of two reacta= nts joined by a dummy atom(using=0A>MOLDEN).Thus I got a single Z-Matrix fo= r reactant complex. when i tried to=0A>do Geometry Optimization for this st= ructure with HF/6-21G*, Charge=3D1, and=0A>Spin Multiplicity=3D2,=0A>the ca= lculation has been terminated with the following error,=0A>"The combination= of Multiplicity 2 and 66 electrons are impossible"=0A>The fault is with mu= ltiplicity. I am not able to resolve this.=0A>=0A>Does anybody tell me how = to find Charge and Multiplicity ingeneral and=0A>charge and multiplicity fo= r the above system.?=0A>=0A>Thanks in advance=0A>=0A>SatheesKannan=0A>M.Tec= h(Chemical Engineering)=0A>Indian Institute of Technology - Kanpur(India)= =0A>email id: satheeskannan---gmail.com=0A=0A=0ARamachandran Chelat,=0D=0AD= ept. of Chemistry,=0D=0AIIT Kanpur=0D=0AKanpur -208016=0D=0APh: +91-512-259= 7367=0D=0A=0D=0Ahttp://home.iitk.ac.in/~ramcn/ --Next_1206718491---0-202.137.234.213-5359 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0ADear SatheesKannan,
=0A
=0AH^+    has no electron
= =0ASo multiplicity should be 1
=0A
=0Amore over,
=0A
=0AI am su= re that you missed some hydrogen atoms while sketching the molecules.
= =0A
=0AButane    CH3-CH2-CH2-CH3 
=0Aisobutane = CH(CH3)3
=0Aprotonation H+
=0A
=0A------------------------------<= BR>=0A          [C8H21]+   
=0A
= =0Atotal number of electrons =3D 68 electrons (your output says 66 !!!!!)=0A
=0A
=0AI am curious to know that where your proton is attaching= with the reactant and the product system (after the job finish :)-  )=
=0A
=0A
=0Ado you mean the simple reaction
=0A
=0A[CH3-CH2-= CH2-CH2^+] + CH(CH3)3 -----> CH3-CH2-CH2-CH3 & (CH3)C^+  ?
= =0A
=0AThat can have 66 electrons
=0A
=0AWhatever be the case,
= =0Aaddition of proton (protonation) or removal of proton (deprotonation),&n= bsp; multiplicity should be 1
=0A
=0A
=0ARamachandran,
=0A
= =0A
=0A
=0AOn Fri, 28 Mar 2008 sathees kannan satheeskannan(_)gmail.c= om wrote :
=0A>Dear Colleagues
=0A>I am using Gaussian program.= I am trying to find Transition State using
=0A>QST2.
=0A>My sy= stem is
=0A>protonated butane + iso-butane ---> butane + protonate= d iso-butane
=0A>I have drawn structure of two reactants joined by a = dummy atom(using
=0A>MOLDEN).Thus I got a single Z-Matrix for reactan= t complex. when i tried to
=0A>do Geometry Optimization for this stru= cture with HF/6-21G*, Charge=3D1, and
=0A>Spin Multiplicity=3D2,
= =0A>the calculation has been terminated with the following error,
=0A= >"The combination of Multiplicity 2 and 66 electrons are impossible= "
=0A>The fault is with multiplicity. I am not able to resolve t= his.
=0A>
=0A>Does anybody tell me how to find Charge and Multi= plicity ingeneral and
=0A>charge and multiplicity for the above syste= m.?
=0A>
=0A>Thanks in advance
=0A>
=0A>SatheesKann= an
=0A>M.Tech(Chemical Engineering)
=0A>Indian Institute of Tec= hnology - Kanpur(India)
=0A>email id: satheeskannan---gmail.com
= =0A=0A

=0A=0A=0ARamachandran Chelat,=0D
=0ADept. of Chemistry,= =0D
=0AIIT Kanpur=0D
=0AKanpur -208016=0D
=0APh: +91-512-2597367= =0D
=0A=0D
=0Ahttp://home.iitk.ac.in/~ramcn/

=0A
3D'Amity'
--Next_1206718491---0-202.137.234.213-5359-- From owner-chemistry@ccl.net Fri Mar 28 13:20:00 2008 From: "Lukasz Cwiklik cwiklik%a%gmail.com" To: CCL Subject: CCL: Need your help about " RESTARTED DUE TO LINMIN FAILURE ". Message-Id: <-36575-080328122624-22703-er1nFeQgxQ3KBxsq40Lppg!^!server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 28 Mar 2008 18:21:39 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik%a%gmail.com] On Fri, Mar 28, 2008 at 3:21 AM, Hongqing He leohhqa/sohu.com wrote: > > Sent to CCL by: "Hongqing He" [leohhq~!~sohu.com] > Dear colleagues, > > There is an error in "Minimising the structure". > > Here is the input file: > intial minimisation solvent + ions > &cntrl > imin = 1, > maxcyc = 1000, > ncyc = 500, > ntb = 1, > cut = 10 > / > Here is a part of the output file: > > NSTEP ENERGY RMS GMAX NAME NUMBER > 1 8.2637E+11 1.0194E+11 2.6974E+13 O 26108 > > BOND = 45960.0689 ANGLE = 1519.6372 DIHED = 3968.5744 > VDWAALS = ************* EEL = -188894.8931 HBOND = 0.0000 > 1-4 VDW = 2165.8427 1-4 EEL = 19481.8190 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 50 -4.8729E+04 1.5562E+02 3.0359E+04 O 45560 > > BOND = 44692.2739 ANGLE = 1763.6515 DIHED = 3988.5936 > VDWAALS = 71542.7480 EEL = -192261.8813 HBOND = 0.0000 > 1-4 VDW = 2126.4422 1-4 EEL = 19419.0077 RESTRAINT = 0.0000 > > > NSTEP ENERGY RMS GMAX NAME NUMBER > 100 -8.9496E+06 2.3719E+09 5.8696E+11 O 7118 [...] > > NSTEP ENERGY RMS GMAX NAME NUMBER > 500 -3.0695E+07 2.8206E+10 6.9800E+12 H2 44119 > > BOND = 39871.3155 ANGLE = 1816.8594 DIHED = 3994.3607 > VDWAALS = 61240.6623 EEL = ************* HBOND = 0.0000 > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 RESTRAINT = 0.0000 > > .... RESTARTED DUE TO LINMIN FAILURE ... > > Does anybody tell me how to solve it? Dear Hongqing, Is seems that you start your minimization from very unoptimal configuration. Your vdW energy is still very high and, the most important, electrostatic energy EEL explodes. So after 500 steps (when the conjugate gradient method starts, NCYC=500) it fails. Most probably, you have close contacts or too small periodic box. If the latter, try to significantly increase your box (let's say, by 1 A) or maybe run NPT before. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Fri Mar 28 13:55:00 2008 From: "Utpal Sarkar utpalchemiitkgp||gmail.com" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36576-080328125411-29204-Umg5wU1zJc42GSdLUaLaFw__server.ccl.net> X-Original-From: "Utpal Sarkar" Content-Type: multipart/alternative; boundary="----=_Part_18597_16255807.1206716558926" Date: Fri, 28 Mar 2008 16:02:38 +0100 MIME-Version: 1.0 Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp,gmail.com] ------=_Part_18597_16255807.1206716558926 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline for 66 electrons the spin multipicity (2S+1 = 2*0 + 1 = 1) is 1 instead of 2. On 3/28/08, sathees kannan satheeskannan * gmail.com < owner-chemistry^^^ccl.net> wrote: > > > Sent to CCL by: "sathees kannan" [satheeskannan:-:gmail.com] > Dear Colleagues > I am using Gaussian program. I am trying to find Transition State using > QST2. > My system is > protonated butane + iso-butane ---> butane + protonated iso-butane > I have drawn structure of two reactants joined by a dummy atom(using > MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to > do Geometry Optimization for this structure with HF/6-21G*, Charge=1, and > Spin Multiplicity=2, > the calculation has been terminated with the following error, > "The combination of Multiplicity 2 and 66 electrons are impossible" > The fault is with multiplicity. I am not able to resolve this. > > Does anybody tell me how to find Charge and Multiplicity ingeneral and > charge and multiplicity for the above system.? > > Thanks in advance > > SatheesKannan > M.Tech(Chemical Engineering) > Indian Institute of Technology - Kanpur(India) > email id: satheeskannan|*|gmail.com> > > ------=_Part_18597_16255807.1206716558926 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
for 66 electrons the spin multipicity (2S+1 = 2*0 + 1 = 1) is 1 instead of 2.
 
 

 
On 3/28/08, sathees kannan satheeskannan * gmail.com <owner-chemistry^^^ccl.net> wrote:

Sent to CCL by: "sathees  kannan" [satheeskannan:-:gmail.com]
Dear Colleagues
I am using Gaussian program. I am trying to find Transition State using QST2.
My system is
protonated butane + iso-butane ---> butane + protonated iso-butane
I have drawn structure of two reactants joined by a dummy atom(using MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to do Geometry Optimization for this structure with HF/6-21G*, Charge=1, and Spin Multiplicity=2,
the calculation has been terminated with the following error,
"The combination of Multiplicity 2 and 66 electrons are impossible"
The fault is with multiplicity. I am not able to resolve this.

Does anybody tell me how to find Charge and Multiplicity ingeneral and charge and multiplicity for the above system.?

Thanks in advance

SatheesKannan
M.Tech(Chemical Engineering)
Indian Institute of Technology - Kanpur(India)
email id: satheeskannan|*|gmail.com



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------=_Part_18597_16255807.1206716558926-- From owner-chemistry@ccl.net Fri Mar 28 14:30:00 2008 From: "Dan Maftei dan.maftei_-_chem.uaic.ro" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36577-080328121853-21939-OmW3bCUamkvS2Pm5JOKwkA _ server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 28 Mar 2008 17:47:34 -0400 Mime-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei ~~ chem.uaic.ro] Hello, again, If is wasn't a typo, the correct route section should contain HF/6-31*, not HF/6-21* (there is no such a basis set defined in Gaussian suite). Dan. On Fri, 2008-03-28 at 17:01 +0530, sathees kannan satheeskannan(_)gmail.com wrote: > Dear Colleagues > I am using Gaussian program. I am trying to find Transition State > using QST2. > My system is > protonated butane + iso-butane ---> butane + protonated iso-butane > I have drawn structure of two reactants joined by a dummy atom(using > MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i > tried to do Geometry Optimization for this structure with HF/6-21G*, > Charge=1, and Spin Multiplicity=2, > the calculation has been terminated with the following error, > "The combination of Multiplicity 2 and 66 electrons are impossible" > The fault is with multiplicity. I am not able to resolve this. > > Does anybody tell me how to find Charge and Multiplicity ingeneral and > charge and multiplicity for the above system.? > > Thanks in advance > > SatheesKannan > M.Tech(Chemical Engineering) > Indian Institute of Technology - Kanpur(India) > email id: satheeskannan---gmail.com From owner-chemistry@ccl.net Fri Mar 28 15:05:00 2008 From: "Dan Maftei dan.maftei*chem.uaic.ro" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36578-080328121853-21925-GaIM8TwCsOSlI1D7R9orkw(0)server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 28 Mar 2008 17:22:27 -0400 Mime-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei]![chem.uaic.ro] Hy, Your system's spin multiplicity should be 1: since you are adding only a proton (positive charge, no electrons) to a neutral system (butane + iso-butane) you are not changing it's spin multiplicity. Best wishes, Dan. On Fri, 2008-03-28 at 17:01 +0530, sathees kannan satheeskannan(_)gmail.com wrote: > Dear Colleagues > I am using Gaussian program. I am trying to find Transition State > using QST2. > My system is > protonated butane + iso-butane ---> butane + protonated iso-butane > I have drawn structure of two reactants joined by a dummy atom(using > MOLDEN).Thus I got a single Z-Matrix for reactant complex. wh en i > tried to do Geometry Optimization for this structure with HF/6-21G*, > Charge=1, and Spin Multiplicity=2, > the calculation has been terminated with the following error, > "The combination of Multiplicity 2 and 66 electrons are impossible" > The fault is with multiplicity. I am not able to resolve this. > > Does anybody tell me how to find Charge and Multiplicity ingeneral and > charge and multiplicity for the above system.? > > Thanks in advance > > SatheesKannan > M.Tech(Chemical Engineering) > Indian Institute of Technology - Kanpur(India) > email id: satheeskannan---gmail.com From owner-chemistry@ccl.net Fri Mar 28 15:40:00 2008 From: "Steve Williams willsd++appstate.edu" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36579-080328115516-8919-PQGpG1Rv7ihgw84RWXtJxA=server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Mar 2008 11:14:43 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd() appstate.edu] Perhaps the problem is that the proton in the protonated butane has no electrons; this would mean that you do not have a radical cation system, and that the spin multiplicity should be 0. This would be consistent with your 66 electrons. Steve Williams sathees kannan satheeskannan * gmail.com wrote: > Sent to CCL by: "sathees kannan" [satheeskannan:-:gmail.com] > Dear Colleagues > I am using Gaussian program. I am trying to find Transition State using QST2. > My system is > protonated butane + iso-butane ---> butane + protonated iso-butane > I have drawn structure of two reactants joined by a dummy atom(using MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i tried to do Geometry Optimization for this structure with HF/6-21G*, Charge=1, and Spin Multiplicity=2, > the calculation has been terminated with the following error, > "The combination of Multiplicity 2 and 66 electrons are impossible" > The fault is with multiplicity. I am not able to resolve this. > > Does anybody tell me how to find Charge and Multiplicity ingeneral and charge and multiplicity for the above system.? > > Thanks in advance > > SatheesKannan > M.Tech(Chemical Engineering) > Indian Institute of Technology - Kanpur(India) > email id: satheeskannan|*|gmail.com> > > From owner-chemistry@ccl.net Fri Mar 28 16:15:01 2008 From: "David Gallagher gallagher.da() gmail.com" To: CCL Subject: CCL:G: Problem in finding Charge and Spin Multiplicity Message-Id: <-36580-080328140928-18935-toXgN18mhGPQCBNiSUFPKA-*-server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 28 Mar 2008 10:11:16 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da:gmail.com] The error message seems correct. With 66 electrons it has to be singlet or triplet. A doublet (Multiplicity=2) would require an odd number of electrons (i.e. radical). David Gallagher CAChe Research At 04:25 AM 3/28/2008, sathees kannan satheeskannan * gmail.com wrote: >Sent to CCL by: "sathees kannan" [satheeskannan:-:gmail.com] >Dear Colleagues >I am using Gaussian program. I am trying to find Transition State using QST2. >My system is >protonated butane + iso-butane ---> butane + protonated iso-butane >I have drawn structure of two reactants joined by a dummy atom(using >MOLDEN).Thus I got a single Z-Matrix for reactant complex. when i >tried to do Geometry Optimization for this structure with HF/6-21G*, >Charge=1, and Spin Multiplicity=2, >the calculation has been terminated with the following error, >"The combination of Multiplicity 2 and 66 electrons are impossible" >The fault is with multiplicity. I am not able to resolve this. > >Does anybody tell me how to find Charge and Multiplicity ingeneral >and charge and multiplicity for the above system.? > >Thanks in advance > >SatheesKannan >M.Tech(Chemical Engineering) >Indian Institute of Technology - Kanpur(India) >email id: satheeskannan|*|gmail.com From owner-chemistry@ccl.net Fri Mar 28 16:51:00 2008 From: "Jiabo Li jiaboli|,|yahoo.com" To: CCL Subject: CCL:G: Too large density matrix to intepret Message-Id: <-36581-080328114243-32158-ioF3J2BcEO3uTw4Pags5Tw%%server.ccl.net> X-Original-From: Jiabo Li Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-253080097-1206715351=:97261" Date: Fri, 28 Mar 2008 07:42:31 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli+*+yahoo.com] --0-253080097-1206715351=:97261 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I am not surprised for the poor results. Generally speaking, when you are using very large and flexible basis set, the usual population analysis methods, especially Mulliken method, give very bad, unphysical results. There are fundamental reasons why this happens. First, partial charge assignment can not be done in an unambiguous way. Second, the ambiguity becomes more serious when the basis functions are strongly overlapping and highly correlated. The problem will be even worse when you are dealing with bad or some exotic structures. Here is my suggestion: if all these happen for your molecule, then forget the Mulliken charges! "Ru Jin lilichemistry^yahoo.com" wrote: Sent to CCL by: "Ru Jin" [lilichemistry[#]yahoo.com] Hi, everyone: I am using Gauusian program G03 doing a single point calculation for C7N( seven carbon atoms and a nytrogen atiom lying on a line) at hf/6-31++g**. The resultant file gives too large value of density matrix on 4s orbital of the carbon atom neighboring the nytrogen atom, ca. 4.7 for alpha and beta respectively, and consequently 17.9 for the condensed number on this carbon atom, which is too large considering that there are only seven electrons around the neutral nytrogen atom. Who could be kindly to show me some principles about resonable value of density matrix, or more general resonable value of basis cofficient among a molecular orbital? Thanks in advance, Ru Jinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-253080097-1206715351=:97261 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
I am not surprised for the poor results. Generally speaking, when you are using very large and flexible basis set, the usual population analysis methods, especially Mulliken method, give very bad, unphysical results. There are fundamental reasons why this happens. First, partial charge assignment can not be done in an unambiguous way. Second, the ambiguity becomes more serious when the basis functions are strongly overlapping and highly correlated. The problem will be even worse when you are dealing with bad or some exotic structures. Here is my suggestion: if all these happen for your molecule, then forget the Mulliken charges!
 


"Ru Jin lilichemistry^yahoo.com" <owner-chemistry%a%ccl.net> wrote:

Sent to CCL by: "Ru Jin" [lilichemistry[#]yahoo.com]
Hi, everyone:
I am using Gauusian program G03 doing a single point calculation for C7N( seven carbon atoms and a nytrogen atiom lying on a line) at hf/6-31++g**. The resultant file gives too large value of density matrix on 4s orbital of the carbon atom neighboring the nytrogen atom, ca. 4.7 for alpha and beta respectively, and consequently 17.9 for the condensed number on this carbon atom, which is too large considering that there are only seven electrons around the neutral nytrogen atom. Who could be kindly to show me some principles about resonable value of density matrix, or more general resonable value of basis cofficient among a molecular orbital?
Thanks in advance,
Ru Jin


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--0-253080097-1206715351=:97261-- From owner-chemistry@ccl.net Fri Mar 28 17:34:00 2008 From: "John McKelvey jmmckel##gmail.com" To: CCL Subject: CCL: Graphics demos Message-Id: <-36582-080328170215-19688-NCClskVcKmBrfACOX/VCYA#%#server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_34843_21033987.1206738122724" Date: Fri, 28 Mar 2008 17:02:02 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel-#-gmail.com] ------=_Part_34843_21033987.1206738122724 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, I am giving a seminar on applications of theory in industry. Now I have done this many times in the past, mostly to undergrad and grad students who are comfortable with theory, though in varying degrees. The next challenge is to give one in an undergraduate department where theory in detail is not appropriate, but I can give some black box descriptions of methods and results. What would be nice, I'm told, would be some appropriate "cool graphics." I'm not strong in the bio/pharma area, but do understand a bit of the importance of docking, etc. Demoing some dynamics results on a simple reaction could be interesting, for example. I'm most receptive to any and all suggestions, and any demos that might be available.. Many thanks!! John McKelvey ------=_Part_34843_21033987.1206738122724 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks,

I am giving a seminar on applications of theory in industry.  Now I have done this many times in the past, mostly to undergrad and grad students  who are comfortable with theory, though in varying degrees.  The next challenge is to give one in an undergraduate department where theory in detail is not appropriate, but I can give some black box descriptions of methods and results.  What would be nice, I'm told, would be some appropriate "cool graphics."  I'm not strong in the bio/pharma area, but do understand a bit of the importance of docking, etc.  Demoing some dynamics results on a simple reaction could be interesting, for example.

I'm most receptive to any and all suggestions, and any demos that might be available..

Many thanks!!

John McKelvey
------=_Part_34843_21033987.1206738122724-- From owner-chemistry@ccl.net Fri Mar 28 19:39:00 2008 From: "Ross Walker ross!^!rosswalker.co.uk" To: CCL Subject: CCL: Need your help about " RESTARTED DUE TO LINMIN FAILURE ". Message-Id: <-36583-080328172208-1389-XJqhZl2QNAfWPRksmtnE9g#server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 28 Mar 2008 13:21:51 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross#,#rosswalker.co.uk] Hi Andrew, Please see: http://amber.scripps.edu/Questions/linmin.html You are also probably better posting questions about amber to the amber mail reflector. See http://amber.scripps.edu for details on how to subscribe. All the best Ross /\ \/ |\oss Walker | Assistant Research Professor | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross() rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. > -----Original Message----- > From: owner-chemistry() ccl.net [mailto:owner-chemistry() ccl.net] > Sent: Friday, March 28, 2008 02:24 > To: Walker, Ross > Subject: CCL: Need your help about " RESTARTED DUE TO LINMIN > FAILURE ". > > > Sent to CCL by: Andrew Turner [andrew.turner**ed.ac.uk] > > Hongqing, > > I think we need some more detail here to be able to help. > What sort of > system are you studying? > > Most often minimization problems are caused by a bad starting > structure. > What sort of configuration are you using? Can you check for bad > contacts? Your electrostatic energy is getting out of control > which is > also suggestive of a bad starting configuration. > > You could try restraining the ions and letting the water relax first > before minimizing the whole system. > > Andy > > Hongqing He leohhqa/sohu.com wrote: > > Sent to CCL by: "Hongqing He" [leohhq~!~sohu.com] > > Dear colleagues, > > > > There is an error in "Minimising the structure". > > > > Here is the input file: > > intial minimisation solvent + ions > > &cntrl > > imin = 1, > > maxcyc = 1000, > > ncyc = 500, > > ntb = 1, > > cut = 10 > > / > > Here is a part of the output file: > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 1 8.2637E+11 1.0194E+11 2.6974E+13 > O 26108 > > > > BOND = 45960.0689 ANGLE = 1519.6372 DIHED > = 3968.5744 > > VDWAALS = ************* EEL = -188894.8931 HBOND > = 0.0000 > > 1-4 VDW = 2165.8427 1-4 EEL = 19481.8190 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 50 -4.8729E+04 1.5562E+02 3.0359E+04 > O 45560 > > > > BOND = 44692.2739 ANGLE = 1763.6515 DIHED > = 3988.5936 > > VDWAALS = 71542.7480 EEL = -192261.8813 HBOND > = 0.0000 > > 1-4 VDW = 2126.4422 1-4 EEL = 19419.0077 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 100 -8.9496E+06 2.3719E+09 5.8696E+11 > O 7118 > > > > BOND = 39871.3056 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6536 EEL = -9078085.4300 HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 150 -1.2010E+07 4.2881E+09 1.0612E+12 > O 7118 > > > > BOND = 39871.3077 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6553 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 200 -7.7833E+07 1.8184E+11 4.4999E+13 > H2 44119 > > > > BOND = 39871.3142 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6611 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 250 -1.4221E+07 6.0226E+09 1.4904E+12 > O 7118 > > > > BOND = 39871.3085 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6561 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 300 -5.3996E+07 8.7448E+10 2.1640E+13 > H2 44119 > > > > BOND = 39871.3146 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6615 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 350 -7.2116E+06 1.5344E+09 3.7971E+11 > H2 44119 > > > > BOND = 39871.3227 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6687 EEL = -7340037.9689 HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 400 -2.0690E+07 1.2787E+10 3.1644E+12 > H2 44119 > > > > BOND = 39871.3166 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6633 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 450 -8.1457E+07 1.9918E+11 4.9291E+13 > O 7118 > > > > BOND = 39871.3125 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6596 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > > > NSTEP ENERGY RMS GMAX > NAME NUMBER > > 500 -3.0695E+07 2.8206E+10 6.9800E+12 > H2 44119 > > > > BOND = 39871.3155 ANGLE = 1816.8594 DIHED > = 3994.3607 > > VDWAALS = 61240.6623 EEL = ************* HBOND > = 0.0000 > > 1-4 VDW = 2110.8874 1-4 EEL = 19406.8604 > RESTRAINT = 0.0000 > > > > .... RESTARTED DUE TO LINMIN FAILURE ... > > > > Does anybody tell me how to solve it? > > > > Thanks a lot. > > > > Hongqing> > > > > > > -- > ================================== > Dr Andrew R. Turner > Research Computing Officer > e: andrew.turner]=[ed.ac.uk > t: +44 (0)131 650 7748 > w: http://www.eastchem.ac.uk/rcf > icq: 370-899-715 > p: School of Chemistry > University of Edinburgh > EH9 3JJ > ================================== > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > > From owner-chemistry@ccl.net Fri Mar 28 20:13:01 2008 From: "Josef Scheiber mail{:}josef-scheiber.de" To: CCL Subject: CCL: LAST Call for PAPERS - Systems Chemical Biology(!)ACS Philadelphia Message-Id: <-36584-080328200258-20090-g/hHM0zXYbU0/cDjQSbwcA(!)server.ccl.net> X-Original-From: Josef Scheiber Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Mar 2008 20:02:26 -0400 MIME-Version: 1.0 Sent to CCL by: Josef Scheiber [mail]~[josef-scheiber.de] Dear Colleagues, This is the last call for abstracts for an exciting symposium at the upcoming ACS meeting in Philadelphia! Rajarshi Guha and I are organizing a symposium focusing on the use of biological networks and their models for the purposes of drug discovery. Traditionally, such models have been applied to large scale biological systems such as protein-protein interaction networks. Recently, there has been increased interest in the study of these networks to gain a global understanding of biological systems and the impact of small molecules to them in the context of drug discovery. As a result, it has become important that such models integrate small molecules with the usual biological systems. By leveraging the power of established cheminformatics methods along with the network models we get closer to the goal of "systems chemical biology", the full integration of chemical and biological data in the development of better in silico-methods for drug discovery. We invite you to submit contributions that address various computational aspects of this approach including, but not limited to: network construction, integration of multiple data sources in network models, drug repurposing, target identification, polypharmacology, incorporation of chemical structure/similarity into network models, bridging chemical structure and biological structure based network models. Case studies where computational network models have provided experimental insight are also welcome. The on-line abstract submission system (OASYS) has already closed for the Fall Meeting. However, you can still mail an abtract to us before April 5th, 2008. The contact information can be found below. So, time to hurry now :-) Please contact Rajarshi or myself if you have any questions. Thanks, Josef Scheiber Novartis josef.scheiber(~)novartis.com Ph: +1-617-871-3697 Rajarshi Guha Indiana University rguha(~)indiana.edu Ph: +1-814-404-5449