From owner-chemistry@ccl.net Thu Sep 17 03:41:00 2009 From: "Chris Swain swain * mac.com" To: CCL Subject: CCL: Ligand based virtual screening and drug design Message-Id: <-40263-090917034009-12803-OLfRVEHICHvqUaqqvdvRCA- -server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Boundary_(ID_RAMurMcTSNTH8ltxC8gTPw)" Date: Thu, 17 Sep 2009 08:39:41 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain[*]mac.com] --Boundary_(ID_RAMurMcTSNTH8ltxC8gTPw) Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-transfer-encoding: 7BIT Hi, I'd also endorse the OpenEye software, easy to use and excellent results. It would also be worth looking at the Cresset software (http://www.cresset-bmd.com/home.shtml ) which offers a rather different approach. Chris Dr Chris Swain Cambridge MedChem Consulting, http://www.cambridgemedchemconsulting.com On 15 Sep 2009, at 16:30, Andrei Leitao ierdna[#]ig.com.br wrote: > Hi, > > For me, the OpenEye set is the best one, with very good results > using ROCS for 3D similarity. > Brood appears to be interesting for bioisosterism, but I did not > try it yet. > Filter is a good tool for reducing the amount of molecules in huge > databanks by means of simple (and useful) rules. > Omega generates quite good conformations in a straightforward way. > Atomic charges can be calculated with Quacpac. > > These programs can be used together, without any costs for academics. > Website: http://www.eyesopen.com > > > Best, > > Andrei > > > > 2009/9/15 Werner K werner.schroedinger(-)googlemail.com chemistry~~ccl.net> > > Sent to CCL by: "Werner K" [werner.schroedinger a googlemail.com] > Hi, > > what is in your opinion the best software packages for ligand based > virtual screening and drug design? > > Thanks > > > > -= This is automatically added to each message by the mailing script > =- > > > > E-mail to subscribers: CHEMISTRY~~ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST~~ccl.net or use> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > > --Boundary_(ID_RAMurMcTSNTH8ltxC8gTPw) Content-type: text/html; charset=US-ASCII Content-transfer-encoding: quoted-printable Hi,

I'd also = endorse the OpenEye software, easy to use and excellent = results.

It would also be worth looking at the = Cresset software (http://www.cresset-bmd.com/= home.shtml) which offers a rather different = approach.

Chris

Dr Chris = Swain
Cambridge MedChem Consulting,

On 15 Sep 2009, at 16:30, = Andrei Leitao ierdna[#]ig.com.br wrote:

 Hi,

 For me, the OpenEye set is the best = one, with very good results using ROCS for 3D similarity.
 Brood = appears to be interesting for bioisosterism, but I did not try it = yet.
 Filter is a good tool for reducing the amount of molecules = in huge databanks by means of simple (and useful) rules.
 Omega = generates quite good conformations in a straightforward = way.
 Atomic charges can be calculated with = Quacpac.

 These programs can be used together, without any = costs for academics.
 Website: http://www.eyesopen.com
=

 Best,

 Andrei



2009/9/15 Werner K werner.schroedinger(-)googlemail.com <owner-chemistry~~ccl.net><= /span>

Sent to CCL by: "Werner  K" [werner.schroedinger a googlemail.com]
= Hi,

what is in your opinion the best software packages for = ligand based virtual screening and drug design?

Thanks

=

-=3D This is automatically added to each message by the = mailing script =3D-



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= --Boundary_(ID_RAMurMcTSNTH8ltxC8gTPw)-- From owner-chemistry@ccl.net Thu Sep 17 04:26:01 2009 From: "Igor Avilov igor.avilov{:}fundp.ac.be" To: CCL Subject: CCL:G: readwa-lseekm error i Gaussian 98 Message-Id: <-40264-090917033635-12444-RpW1TXXOhVhPF5hZTHDWGg*server.ccl.net> X-Original-From: Igor Avilov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Sep 2009 09:06:48 +0200 MIME-Version: 1.0 Sent to CCL by: Igor Avilov [igor.avilov{=}fundp.ac.be] Hi, I had "writwa" message once. It was an old problem. It was solved in G03. The problem was related to the read-write file, which should be split on 2GB chunks (up to 8 chunks) approximately as follows: %rwf=a,245mw,b,245mw,c,245mw,d,245mw,e,245mw,f,245mw,g,245mw,h,245mw Probably, "readwa-lseekm" has the same solution... Best wishes, Igor. Babak Khalili Hadad khalili.babak : gmail.com wrote: > Sent to CCL by: "Babak Khalili Hadad" [khalili.babak[#]gmail.com] > Dear Subscribers, > > I have done a calculation on Gaussian98 under windows to hold freq analysis. Unfortunately, the error of wrtitewa occurs all times. > I increases the memory by $FREQMEM and again the writewa appeared, again I do increase of %mem=100mw but the "readwa-lseekm" is appeared now. May you lead me to solve this problem? > You can see the following as an example. > > Best regards, > Babak Khalili > > > Inv2: IOpt= 1 Iter= 1 AM= 7.50D-16 Conv= 1.00D-12. > Inverted reduced A of dimension 42 with in-core refinement. > G2DrvN: will do 132 atoms at a time, making 1 passes doing MaxLOS=1. > FoFDir used for L=0 through L=1. > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > Integrals replicated using symmetry in FoFDir. > MinBra= 0 MaxBra= 1 Meth= 1. > IRaf= 0 NMat= 399 IRICut= 82 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. > Raff turned off since only 32.11% of shell-pairs survive. > There are 399 degrees of freedom in the 1st order CPHF. > 396 vectors were produced by pass 0. > AX will form 396 AO Fock derivatives at one time. > 396 vectors were produced by pass 1. > readwa-lseekm> > > -- ------------------------------------------------ Igor Avilov Université de Namur (FuNDP) Centre de Recherche en Physique de la Matière et du Rayonnement (PMR) Laboratoire LISE 61, Rue de Bruxelles B-5000 Namur (Belgium) Tél: +32 81 72 52 32 Fax: +32 81 72 45 95 E-mail: igor.avilov . fundp.ac.be web:http://www.fundp.ac.be/en/sci/physics/lise/ ------------------------------------------------ *********************************** Visit our EU projects' websites: http://www.icontrol-strep.eu/ http://www.nano2hybrids.net/ *********************************** From owner-chemistry@ccl.net Thu Sep 17 07:27:01 2009 From: "mehdi baayt mehdi806##gmail.com" To: CCL Subject: CCL:G: A Problem on calculation of BSSE in l401 Message-Id: <-40265-090917034008-12789-45+WiJ0bToPPJA+Uan16BA a server.ccl.net> X-Original-From: "mehdi baayt" Date: Thu, 17 Sep 2009 03:40:04 -0400 Sent to CCL by: "mehdi baayt" [mehdi806 * gmail.com] Dear Sir/madam Hi I was attempting to run a single point calulation using B3LYP/LANL2MB scf=tight Massage on a metal complexes(ML) for this I should freeze the atoms in two parts in the first central metal ion(M)with (4 Nuc 0.0 in the end of input file) and again in other file freeze all of atoms of ligand(L) expect central metal ion but in the first I can calculate the energy for first step(freeze the metal ion with 4 Nuc 0.0)but in second when I freezed the all of atoms of ligand(L) expect central metal ion(with key words 1 Nuc 0.0 2 nuc 0.0 and etc) I contact with this problem as below: Symmetry turned off by external request. Stoichiometry Framework group Deg. of freedom 120 Full point group C1 NOp 1 Rotational constants (GHZ): 0.3682135 0.3008676 0.1739130 Standard basis: LANL2MB (5D, 7F) The nuclear charge for atom 1 has been changed to Z= 0 0.000000 The nuclear charge for atom 2 has been changed to Z= 0 0.000000 The nuclear charge for atom 3 has been changed to Z= 0 0.000000 The nuclear charge for atom 5 has been changed to Z= 0 0.000000 The nuclear charge for atom 6 has been changed to Z= 0 0.000000 The nuclear charge for atom 7 has been changed to Z= 0 0.000000 The nuclear charge for atom 8 has been changed to Z= 0 0.000000 The nuclear charge for atom 9 has been changed to Z= 0 0.000000 The nuclear charge for atom 10 has been changed to Z= 0 0.000000 The nuclear charge for atom 11 has been changed to Z= 0 0.000000 The nuclear charge for atom 12 has been changed to Z= 0 0.000000 The nuclear charge for atom 13 has been changed to Z= 0 0.000000 The nuclear charge for atom 14 has been changed to Z= 0 0.000000 The nuclear charge for atom 15 has been changed to Z= 0 0.000000 The nuclear charge for atom 16 has been changed to Z= 0 0.000000 The nuclear charge for atom 16 has been changed to Z= 0 0.000000 The nuclear charge for atom 17 has been changed to Z= 0 0.000000 The nuclear charge for atom 18 has been changed to Z= 0 0.000000 The nuclear charge for atom 19 has been changed to Z= 0 0.000000 The nuclear charge for atom 20 has been changed to Z= 0 0.000000 The nuclear charge for atom 21 has been changed to Z= 0 0.000000 The nuclear charge for atom 22 has been changed to Z= 0 0.000000 The nuclear charge for atom 23 has been changed to Z= 0 0.000000 The nuclear charge for atom 24 has been changed to Z= 0 0.000000 The nuclear charge for atom 25 has been changed to Z= 0 0.000000 The nuclear charge for atom 26 has been changed to Z= 0 0.000000 The nuclear charge for atom 27 has been changed to Z= 0 0.000000 The nuclear charge for atom 28 has been changed to Z= 0 0.000000 The nuclear charge for atom 29 has been changed to Z= 0 0.000000 The nuclear charge for atom 30 has been changed to Z= 0 0.000000 The nuclear charge for atom 31 has been changed to Z= 0 0.000000 The nuclear charge for atom 32 has been changed to Z= 0 0.000000 The nuclear charge for atom 33 has been changed to Z= 0 0.000000 The nuclear charge for atom 34 has been changed to Z= 0 0.000000 The nuclear charge for atom 35 has been changed to Z= 0 0.000000 The nuclear charge for atom 36 has been changed to Z= 0 0.000000 The nuclear charge for atom 37 has been changed to Z= 0 0.000000 The nuclear charge for atom 38 has been changed to Z= 0 0.000000 The nuclear charge for atom 39 has been changed to Z= 0 0.000000 The nuclear charge for atom 40 has been changed to Z= 0 0.000000 The nuclear charge for atom 41 has been changed to Z= 0 0.000000 The nuclear charge for atom 42 has been changed to Z= 0 0.000000 Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 125 basis functions, 375 primitive gaussians, 125 cartesian basis functions 0 alpha electrons 0 beta electrons nuclear repulsion energy 0.0000000000 Hartrees. NAtoms= 42 NActive= 42 NUniq= 42 SFac= 1.00D+00 NAtFMM= 60 Big=F One-electron integrals computed using PRISM. 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 2016 NPrTT= 18144 LenC2= 1874 LenP2D= 11313. LDataN: DoStor=F MaxTD1= 3 Len= 28 LDataN: DoStor=T MaxTD1= 3 Len= 28 NBasis= 125 RedAO= T NBF= 125 NBsUse= 125 1.00D-06 NBFU= 125 Harris functional with IExCor= 402 diagonalized for initial guess. ExpMin= 4.04D-02 ExpMax= 1.31D+02 ExpMxC= 1.31D+02 IAcc=2 IRadAn= 4 AccDes= 0.00D+00 HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 4 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Warning: off-atom basis functions, so minimal bfn integration tests in XC quadrature. Spurious integrated density or basis function: NE= 12 NElCor= 0 El error=7.21D-08 rel=6.01D-09 Tolerance=1.00D-03 Shell 9 absolute error=3.68D+01 Tolerance=no limit Shell 9 signed error=3.68D+01 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in d:\g03-new\l401.exe at Thu Sep 17 11:37:01 2009. Job cpu time: 0 days 0 hours 0 minutes 9.0 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 Please help me Regards. From owner-chemistry@ccl.net Thu Sep 17 09:43:01 2009 From: "Yang Mingjun jeffle07|a|163.com" To: CCL Subject: CCL: The correlation analysis Message-Id: <-40266-090916095304-30529-7fC7NX8NTvcbdFZAU2qSAA() server.ccl.net> X-Original-From: "Yang Mingjun" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Wed, 16 Sep 2009 21:07:15 +0800 Mime-Version: 1.0 Sent to CCL by: "Yang Mingjun" [jeffle07,+,163.com] Dear all, We performed a MD simulation of a protein system. Now we are going to check the correlated motion between one part of the protein (e.g. one residue) and another part (e.g. another residue) based on the generated trajectories. Any one who can recommend a method for this purpose? Many thanks. Jeffrey --- DICP, CHINA From owner-chemistry@ccl.net Thu Sep 17 10:17:01 2009 From: "Atul Agarwal aagarwal[A]achillion.com" To: CCL Subject: CCL: Ligand based virtual screening and drug design Message-Id: <-40267-090917091236-3451-Gg8xW40bhMdebL2AiQ5nfg{:}server.ccl.net> X-Original-From: "Atul Agarwal" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Thu, 17 Sep 2009 08:39:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Atul Agarwal" [aagarwal],[achillion.com] I used the LASSO (http://www.simbiosys.ca/ehits_lasso/) approach for ligand based virtual screening in the past year. I think it is an attractive approach with a novel 2.5 D descriptor combined with very fast neural network based screening engine. More information about the method is in the following publication: D. Reid, B. S. Sadjad, Z. Zsoldos, A. Simon: LASSO - ligand activity by surface similarity order: a new tool for ligand based virtual screening Journal of Computer-Aided Molecular Design http://dx.doi.org/10.1007/s10822-007-9164-5 doi: 10.1007/s10822-007-9164-5 Atul Agarwal Senior Director, CCI Achillion Pharmaceuticals, Inc. 300 George Street New Haven, CT 06511 203-752-5491 (tel) 203-752-5454 (FAX) aagarwal-x-achillion.com -----Original Message----- > From: owner-chemistry+aagarwal=3D=3Dachillion.com-x-ccl.net [mailto:owner-chemistry+aagarwal=3D=3Dachillion.com-x-ccl.net] On Behalf = Of Werner K werner.schroedinger(-)googlemail.com Sent: Tuesday, September 15, 2009 9:18 AM To: Atul Agarwal Subject: CCL: Ligand based virtual screening and drug design Sent to CCL by: "Werner K" [werner.schroedinger a googlemail.com] Hi, what is in your opinion the best software packages for ligand based virtual screening and drug design? Thanks -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Sep 17 11:28:00 2009 From: "kavi sona kavisona7..googlemail.com" To: CCL Subject: CCL: M-L back bonding Message-Id: <-40268-090917110230-6259-tVGtrsVZdj8ck9dqQyAysA * server.ccl.net> X-Original-From: "kavi sona" Date: Thu, 17 Sep 2009 11:02:26 -0400 Sent to CCL by: "kavi sona" [kavisona7]![googlemail.com] Dear All, How can one interpret M-L back bonding with the NBO analysis? Could any one post some related articles? Thank you, Kavi From owner-chemistry@ccl.net Thu Sep 17 12:16:01 2009 From: "yvonnecmartin(_)comcast.net" To: CCL Subject: CCL: Ligand based virtual screening and drug design Message-Id: <-40269-090917120336-2948-0sEyjj/EU0Is84zfAmI13w|*|server.ccl.net> X-Original-From: yvonnecmartin|*|comcast.net Content-Type: multipart/alternative; boundary="----=_Part_110255_1709012563.1253201446048" Date: Thu, 17 Sep 2009 15:30:46 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: yvonnecmartin\a/comcast.net ------=_Part_110255_1709012563.1253201446048 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi all,=20 Steve Muchmore and I did a comparison of a number of tools. Bottom line: no= one approach works well for "lead hopping", that is finding really differe= nt molecules. We now use a combination of ROCS and SciTegic EPF6 fingerprin= ts, combined with a Belief Theory algorithm. This work is published in QSAR= and Combinatorial Chemistry approximately nine months ago. I am happy to s= end more information off-line.=20 Yvonne Martin=20 ----- Original Message -----=20 > From: "Andrei Leitao ierdna[#]ig.com.br" =20 To: "Yvonne Martin" =20 Sent: Tuesday, September 15, 2009 10:30:03 AM GMT -06:00 US/Canada Central= =20 Subject: CCL: Ligand based virtual screening and drug design=20 =C2=A0Hi,=20 =C2=A0For me, the OpenEye set is the best one, with very good results using= ROCS for 3D similarity.=20 =C2=A0Brood appears to be interesting for bioisosterism, but I did not try = it yet.=20 =C2=A0Filter is a good tool for reducing the amount of molecules in huge da= tabanks by means of simple (and useful) rules.=20 =C2=A0Omega generates quite good conformations in a straightforward way.=20 =C2=A0Atomic charges can be calculated with Quacpac.=20 =C2=A0These programs can be used together, without any costs for academics.= =20 =C2=A0Website: http://www.eyesopen.com=20 =C2=A0Best,=20 =C2=A0Andrei=20 2009/9/15 Werner K werner.schroedinger(-) googlemail.com < owner-chemistry~= ~ccl.net >=20 Sent to CCL by: "Werner =C2=A0K" [werner.schroedinger a googlemail.com ]=20 Hi,=20 what is in your opinion the best software packages for ligand based virtual= screening and drug design?=20 Thanks=20 -=3D This is automatically added to each message by the mailing script =3D-= =20 E-mail to subscribers: CHEMISTRY~~ccl.net or use:=20 =C2=A0 =C2=A0 =C2=A0=20 E-mail to administrators: CHEMISTRY-REQUEST~~ccl.net or use=20 =C2=A0 =C2=A0 =C2=A0=20 Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0=20=20 Job: http://www.ccl.net/jobs=20=20=20 =C2=A0 =C2=A0 =C2=A0=20=20 ------=_Part_110255_1709012563.1253201446048 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <= div style=3D'font-family: Arial; font-size: 12pt; color: #000000'>

Hi all= ,

 

Steve Muchmore and I did a comparison of a number of tools. Bottom line:= no one approach works well for "lead hopping", that is finding really diff= erent molecules. We now use a combination of ROCS and SciTegic EPF6 fingerp= rints, combined with a Belief Theory algorithm. This work is published in Q= SAR and Combinatorial Chemistry approximately nine months ago. I am happy t= o send more information off-line.

 

Yvonne Martin


----- Original Message -----
From: "Andrei Leitao ierdna[#]ig.com= .br" <owner-chemistry*|*ccl.net>
To: "Yvonne Martin" <yv= onnecmartin*|*comcast.net>
Sent: Tuesday, September 15, 2009 10:30:03 A= M GMT -06:00 US/Canada Central
Subject: CCL: Ligand based virtual screen= ing and drug design

 Hi,

 For me, the OpenEye set i= s the best one, with very good results using ROCS for 3D similarity.
&nb= sp;Brood appears to be interesting for bioisosterism, but I did not try it = yet.
 Filter is a good tool for reducing the amount of molecules in= huge databanks by means of simple (and useful) rules.
 Omega gener= ates quite good conformations in a straightforward way.
 Atomic cha= rges can be calculated with Quacpac.

 These programs can be use= d together, without any costs for academics.
 Website: http://www.eyesopen.com

 Best,

 Andrei



2009/9/15 Werner K werner.schroedinger(-)googlemail.com <owner-c= hemistry~~ccl.net>

Sent to CCL by: "W= erner  K" [werner.schroedinger a googlemail.com]
Hi,

what is in your opinion the= best software packages for ligand based virtual screening and drug design?=

Thanks



-=3D This is automatically added to each mess= age by the mailing script =3D-

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------=_Part_110255_1709012563.1253201446048-- From owner-chemistry@ccl.net Thu Sep 17 13:56:00 2009 From: "Nilesh Tawari tawari.nilesh=gmail.com" To: CCL Subject: CCL: Query regarding MOPAC THERMO calculations Message-Id: <-40270-090917135405-14732-mpnnPQq8pbjI8iPlhYI9kA+*+server.ccl.net> X-Original-From: "Nilesh Tawari" Date: Thu, 17 Sep 2009 13:54:01 -0400 Sent to CCL by: "Nilesh Tawari" [tawari.nilesh()gmail.com] Hi, I am using "Thermo" keyword in MOPAC2009 for thermodynamic calculations, but I getting an error GRADIENT NORM = 251.47110 ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, (LIMIT=10) ** EITHER ADD 'LET' OR REDUCE GRADIENT USING 'TS' OR OTHER GEOMETRY OPTIMIZER So i used "LET" keyword, the job was completed but output shows following warning.... GRADIENT NORM = 250.61397 ** GRADIENT IS VERY LARGE, BUT SINCE "LET" IS USED, CALCULATION WILL CONTINUE **** WARNING **** GRADIENT IS VERY LARGE FOR A THERMO CALCULATION RESULTS ARE LIKELY TO BE INACCURATE IF THERE ARE ANY LOW-LYING VIBRATIONS (LESS THAN ABOUT 400CM-1) GRADIENT NORM SHOULD BE LESS THAN ABOUT 0.2 FOR THERMO TO GIVE ACCURATE RESULTS And the calculated heat of formation is too high H.O.F. KCAL/MOL = 241.996 Any comments suggestions on this?? Regards -nilesh From owner-chemistry@ccl.net Thu Sep 17 15:26:01 2009 From: "Michael K. Gilson gilson . umbi.umd.edu" To: CCL Subject: CCL: The correlation analysis Message-Id: <-40271-090917151710-14647-fu8uzdnEUmb8r6VkqsXZhw{:}server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=GB2312 Date: Thu, 17 Sep 2009 14:23:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson^^umbi.umd.edu] We have developed a mutual information approach for this purpose. You could try our ACCENT software, which is freely available here: http://gilsonlab.umbi.umd.edu/software1a.html The main publication is ref #3 on the same web-page. Regards, Mike Yang Mingjun jeffle07|a|163.com wrote: > Sent to CCL by: "Yang Mingjun" [jeffle07,+,163.com] > > Dear all, > > We performed a MD simulation of a protein system. Now we are going to check the correlated motion between one part of the protein (e.g. one residue) and another part (e.g. another residue) based on the generated trajectories. Any one who can recommend a method for this purpose? > > Many thanks. > > Jeffrey > --- > DICP, CHINA> > > > -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu Lab Page: gilsonlab.umbi.umd.edu BindingDB: www.bindingdb.org From owner-chemistry@ccl.net Thu Sep 17 16:01:01 2009 From: "John McKelvey jmmckel(0)gmail.com" To: CCL Subject: CCL: Query regarding MOPAC THERMO calculations Message-Id: <-40272-090917153220-1611-gZpXEmPpgqrQNFY3DBy5tQ%x%server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0016e68debb72a7fb40473cb122e Date: Thu, 17 Sep 2009 15:32:07 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel^gmail.com] --0016e68debb72a7fb40473cb122e Content-Type: text/plain; charset=ISO-8859-1 The geometry is not sufficiently optimized... Do that first, if not done already. If you have then take the geometry at the end of the filename.ARC file and feed that back through. Cheers! John McKelvey On Thu, Sep 17, 2009 at 1:54 PM, Nilesh Tawari tawari.nilesh=gmail.com < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh()gmail.com] > Hi, > I am using "Thermo" keyword in MOPAC2009 for thermodynamic calculations, > but I getting an error > > GRADIENT NORM = 251.47110 > ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, > (LIMIT=10) ** > EITHER ADD 'LET' OR REDUCE GRADIENT > USING 'TS' OR OTHER GEOMETRY OPTIMIZER > > So i used "LET" keyword, the job was completed but output shows following > warning.... > > > GRADIENT NORM = 250.61397 > > ** GRADIENT IS VERY LARGE, BUT SINCE "LET" IS USED, CALCULATION WILL > CONTINUE > > **** WARNING **** > > GRADIENT IS VERY LARGE FOR A THERMO CALCULATION > RESULTS ARE LIKELY TO BE INACCURATE IF THERE ARE > ANY LOW-LYING VIBRATIONS (LESS THAN ABOUT 400CM-1) > GRADIENT NORM SHOULD BE LESS THAN ABOUT 0.2 FOR THERMO > TO GIVE ACCURATE RESULTS > > And the calculated heat of formation is too high H.O.F. KCAL/MOL = 241.996 > > Any comments suggestions on this?? > > Regards > -nilesh> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel*gmail.com --0016e68debb72a7fb40473cb122e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The geometry is not sufficiently optimized... Do that first, if not done al= ready.=A0 If you have then take the geometry at the end of the filename.ARC= file and feed that back through.

Cheers!

John McKelvey
On Thu, Sep 17, 2009 at 1:54 PM, Nilesh Tawari t= awari.nilesh=3Dgmail.com <owner-chemistry*ccl.net= > wrote:

Sent to CCL by: "Nilesh =A0 Tawari" [tawari.nilesh()gmail.com]
Hi,
I am using "Thermo" keyword in MOPAC2009 for thermodynamic calcul= ations, but I getting an error

GRADIENT NORM =3D 251.47110
=A0** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, (LIMIT= =3D10) **
=A0EITHER ADD 'LET' OR REDUCE GRADIENT
=A0USING 'TS' OR OTHER GEOMETRY OPTIMIZER

So i used "LET" keyword, the job was completed but output shows f= ollowing warning....


=A0 =A0 =A0 =A0 =A0GRADIENT NORM =3D 250.61397

=A0** GRADIENT IS VERY LARGE, BUT SINCE "LET" IS USED, CALCULATIO= N WILL CONTINUE

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0**** WARNING **= **

=A0 =A0 =A0 =A0 =A0 GRADIENT IS VERY LARGE FOR A THERMO CALCULATION
=A0 =A0 =A0 =A0 =A0 RESULTS ARE LIKELY TO BE INACCURATE IF THERE ARE
=A0 =A0 =A0 =A0 =A0 ANY LOW-LYING VIBRATIONS (LESS THAN ABOUT 400CM-1)
=A0 =A0 =A0 =A0 =A0 GRADIENT NORM SHOULD BE LESS THAN ABOUT 0.2 FOR THERMO=
=A0 =A0 =A0 =A0 =A0 TO GIVE ACCURATE RESULTS

And the calculated heat of formation is too high =A0H.O.F. KCAL/MOL =3D 241= .996

Any comments suggestions on this??

Regards
-nilesh



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--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel*gmail.com
--0016e68debb72a7fb40473cb122e-- From owner-chemistry@ccl.net Thu Sep 17 16:37:01 2009 From: "Kalju Kahn kalju__chem.ucsb.edu" To: CCL Subject: CCL: The correlation analysis Message-Id: <-40273-090917122050-13028-Qw0ZmFsuct8Yi8MCTfh6OQ\a/server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 17 Sep 2009 09:20:35 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju*o*chem.ucsb.edu] Jeffrey, If I recall correctly, CHARMM had a built-in function for getting the covariance matrix from the trajectory. I used GMT (http://gmt.soest.hawaii.edu/) to plot these on a 2D contour map. You can use Mathematica/Matlab for this as well. In addition, you can color-map the correlated motion on the structure (see http://www.chem.ucsb.edu/~kalju/catalysis.html for details). If you decide to do the latter, please quote my paper (or correct me if I was not the first one do think of this) in J. Am. Chem. Soc., 2001, 123 (48), pp 11960–11969 Best luck, Kalju > > Sent to CCL by: "Yang Mingjun" [jeffle07,+,163.com] > > Dear all, > > We performed a MD simulation of a protein system. Now we are going to > check the correlated motion between one part of the protein (e.g. one > residue) and another part (e.g. another residue) based on the generated > trajectories. Any one who can recommend a method for this purpose? > > Many thanks. > > Jeffrey > --- > DICP, CHINA> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Thu Sep 17 17:11:00 2009 From: "Marcel Swart marcel.swart||icrea.es" To: CCL Subject: CCL: Query regarding MOPAC THERMO calculations Message-Id: <-40274-090917160408-18159-SdqPor9dCaK7jOVvNTkRhA^^^server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 17 Sep 2009 21:59:22 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart:+:icrea.es] A gradient norm of 251.5 is exceptionally large, which indeed is good of Mopac to stop doing the frequency calculation. Note that the whole concept of "Thermo" holds in principle only for zero gradient ! More important than looking at why Mopac does not calculate the Thermodynamic properties (which in my opinion is correct indeed), is the question: why is the gradient so large ? I think you should focus first on optimizing the geometry, and severely reducing the gradient; when Mopac has finished the optimization, the gradient norm should be way below the threshold value of 10.0 for doing the frequency (and hence thermodynamic) calculation. A typical value one would obtain for the gradient norm is below 1.0. Quoting "Nilesh Tawari tawari.nilesh=3Dgmail.com" : > Hi, > I am using "Thermo" keyword in MOPAC2009 for thermodynamic =20 > calculations, but I getting an error > > GRADIENT NORM =3D 251.47110 > ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, =20 > (LIMIT=3D10) ** > EITHER ADD 'LET' OR REDUCE GRADIENT > USING 'TS' OR OTHER GEOMETRY OPTIMIZER > > So i used "LET" keyword, the job was completed but output shows =20 > following warning.... > > > GRADIENT NORM =3D 250.61397 > > ** GRADIENT IS VERY LARGE, BUT SINCE "LET" IS USED, CALCULATION =20 > WILL CONTINUE > > **** WARNING **** > > GRADIENT IS VERY LARGE FOR A THERMO CALCULATION > RESULTS ARE LIKELY TO BE INACCURATE IF THERE ARE > ANY LOW-LYING VIBRATIONS (LESS THAN ABOUT 400CM-1) > GRADIENT NORM SHOULD BE LESS THAN ABOUT 0.2 FOR THERMO > TO GIVE ACCURATE RESULTS > > And the calculated heat of formation is too high H.O.F. KCAL/MOL =3D 241.= 996 > > Any comments suggestions on this?? > > Regards > -nilesh =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=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart=-=icrea.es marcel.swart=-=udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =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=3D=3D=3D=3D=3D=3D