From owner-chemistry@ccl.net Thu Mar 27 04:04:00 2008 From: "Karl Kirschner kkirschn[A]hamilton.edu" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36559-080327034928-11151-QD1Yd4yUu67JmcAp0LkI7A---server.ccl.net> X-Original-From: Karl Kirschner Content-type: multipart/alternative; boundary="Boundary_(ID_6Oskde0BpcU+24xnBH+KqA)" Date: Thu, 27 Mar 2008 07:48:26 +0100 MIME-version: 1.0 Sent to CCL by: Karl Kirschner [kkirschn ~ hamilton.edu] --Boundary_(ID_6Oskde0BpcU+24xnBH+KqA) Content-type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-transfer-encoding: 7BIT Hi Junjun, I sympathize with your dilemma. We also have a need for comparing how similar two different molecules are, specifically how similar is a conserved four amino acid sequence in different peptides (e.g. the similarity between the TPVN sequences in the peptides EMTPVNPG and EKTPVNPGN). For my work, ProFit by Andrew Martin work very well and is versatile. You can download ProFit at http://www.bioinf.org.uk/. Just so you know, in our publications we chose to cite the program as,"Martin, A. C. R. ProFit Version 2.5. 2006, http:// www.bioinf.org.uk/software/profit/." Cheers, Karl ____________________________________ Karl N. Kirschner, Ph.D. Center for Molecular Design, Co-Director Hamilton College, Clinton NY 13323 ____________________________________ On Mar 26, 2008, at 11:02 PM, JunJun Liu ljjlp03]~[gmail.com wrote: > 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 how to do this? Any suggestions regarding algorithms > or softwares are highly appreciated! > > Thanks in advance! > > Junjun --Boundary_(ID_6Oskde0BpcU+24xnBH+KqA) Content-type: text/html; charset=ISO-8859-1 Content-transfer-encoding: quoted-printable Hi = Junjun,

= I=A0sympathize=A0with your=A0dilemma. We also = have a need for comparing how similar two different molecules are, = specifically how similar is a conserved four amino acid sequence in = different peptides (e.g. the similarity between the TPVN sequences in = the peptides EMTPVNPG and EKTPVNPGN). For my work, ProFit by Andrew = Martin work very well and is=A0versatile. You can download ProFit = at=A0http://www.bioinf.org.uk/. Just so = you know, in our publications we chose to cite the program = as,"Martin, A. C. R. = ProFit Version 2.5. 2006, http://www.bioinf.org.uk/software/profit/."=

Cheers,

Karl

Karl N. Kirschner, Ph.D.

Center for Molecular Design, Co-Director

Hamilton College, Clinton NY = 13323

On = Mar 26, 2008, at 11:02 PM, JunJun Liu ljjlp03]~[gmail.com = wrote:

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 how to do this? Any suggestions regarding = algorithms or softwares are highly appreciated!

Thanks = in advance!

Junjun

= --Boundary_(ID_6Oskde0BpcU+24xnBH+KqA)-- From owner-chemistry@ccl.net Thu Mar 27 06:04:01 2008 From: "Carsten Wittekindt wittekindt!A!cosmologic.de" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36560-080327054901-10856-pzYVOMTxrbtVkkD1ukl2+g[*]server.ccl.net> X-Original-From: Carsten Wittekindt Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Thu, 27 Mar 2008 10:50:22 +0100 MIME-Version: 1.0 Sent to CCL by: Carsten Wittekindt [wittekindt!^!cosmologic.de] Dear Junjun! Similarity of molecules is a broad field in chemoinformatics. Therefore, th= ere=20 are and will be lot's of different methods and you need to specify the term= =20 =E2=80=9Csimilarity=E2=80=9D. Do you want to compare size and shape of mole= cules, certain=20 thermodynamic properties or physicochemical behaviour? If you are interested in physicochemical behaviour I'd like to direct your= =20 interest to our COSMO-RS theory. The COSMO-RS theory has shown that the=20 sigma-profiles, which is the representation the charge distribution on the= =20 surface of the molecules, provide crucial information for most=20 physicochemical behaviour. Suitable sigma-profiles are a necessary (though= =20 not sufficient) precondition for good receptor binding. We therefore=20 developed COSMOsim for bio-isoster search. Since the similarity search is=20 based on surface polarity, not on chemical similarity, scaffold hopping is= =20 automatically included.=20 Please visit our homepage and contact us for further information and a free= =20 trial version. http://www.cosmologic.de/LifeScience/cosmosim.html http://www.cosmologic.de/LifeScience/ex_ovSim.html info(at)cosmologic.de All the best Carsten =2D-=20 Dr. Carsten Wittekindt COSMOlogic GmbH & Co. KG Phone +49-2171-363667 Burscheider Str. 515 Fax +49-2171-73168-9 D-51381 Leverkusen Email wittekindt,,cosmologic.de Germany Web http://www.cosmologic.de Am Mittwoch, 26. M=C3=A4rz 2008 23:02 schrieb JunJun Liu ljjlp03]~[gmail.co= m: > 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 > how to do this? Any suggestions regarding algorithms or softwares are > highly appreciated! > > Thanks in advance! > > Junjun > > > > -=3D This is automatically added to each message by the mailing script = =3D- From owner-chemistry@ccl.net Thu Mar 27 07:42:00 2008 From: "Carsten Detering detering++biosolveit.de" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36561-080327073116-29210-nAxgjRwRFgqwAVWT8rYd0Q-#-server.ccl.net> X-Original-From: "Carsten Detering" Date: Thu, 27 Mar 2008 07:31:11 -0400 Sent to CCL by: "Carsten Detering" [detering[A]biosolveit.de] Hi Junjun, try FTrees. FTrees is a software to calculate the similarity of two molecules based on their physico-chemical behavior. It basically aligns two (or more) molecules to each other and calculates a score based on the underlying feature tree descriptor. The latter represents the molecule as a tree with certain nodes, which contain the information of the underlying molecular structure. Due to these nodes, the feature tree brings in a certain degree of fuzzyness, which allows to scaffold hopp across chemical classes. To read more about FTrees or to try it out, please visit www.biosolveit.de/ftrees. You could also use FlexS (www.biosolveit.de/flexs) to align your molecules in 3D and then rank sort the results based on their score. Hope this helps, Carsten __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering-x-biosolveit.com Phone EU: +49-2241-2525-0 / Fax: -525 www.biosolveit.com Phone US: +1-617-297-2770 BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 Am Mittwoch, 26. Mrz 2008 23:02 schrieb JunJun Liu ljjlp03]~[gmail.com: > 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 how to do this? Any suggestions regarding algorithms or softwares > are highly appreciated! > > Thanks in advance! > > Junjun > > > From owner-chemistry@ccl.net Thu Mar 27 08:16:00 2008 From: "Barbara Jagoda-Cwiklik barbara(-)fh.huji.ac.il" To: CCL Subject: CCL:G: PCM problems Message-Id: <-36562-080327075430-3545-Yz55mH/NEoc1dA2geEAyXg__server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 27 Mar 2008 13:53:48 +0200 MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara##fh.huji.ac.il] Ahoj Pavlina :-) There are at least two remedies for the problem (error with link 301) you reported: 1. use NoSymm keyword 2. change a cavity paramters, see here for details: http://server.ccl.net/chemistry/resources/messages/2006/03/02.003-dir/index.html Best regards and good luck, Basia -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara%x%fh.huji.ac.il On Wed, Mar 26, 2008 at 6:28 PM, Pavlina KOSINOVA nu.pavlina^^centrum.cz wrote: > > Sent to CCL by: "Pavlina KOSINOVA" [nu.pavlina::centrum.cz] > Dear CCL Subscribers, > > I am using PCM for radical calculations, i.e., I am just using, as an input command, the default parameters: > > #p ub3p86/6-31g(d) opt freq scrf=(iefpcm,solvent=water) geom=connectivity > > Some of my caculations crashed with the following error message: > > Polarizable Continuum Model (PCM) > ================================= > Model : PCM. > Atomic radii : UA0 (Simple United Atom Topological Model). > Polarization charges : Total charges. > Charge compensation : None. > Solution method : Matrix inversion. > Cavity : GePol (RMin=0.200 OFac=0.890). > Default sphere list used, NSphG= 22. > Tesserae with average area of 0.200 Ang**2. > 1st derivatives : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=0). > Cavity 1st derivative terms included. > Solvent : Water, Eps = 78.390000 > Eps(inf)= 1.776000 > RSolv = 1.385000 Ang. > ------------------------------------------------------------------------------ > AdVTs1: ISph= 500 is engulfed by JSph= 501 but Ae( 500) is not yet zero! > Error termination via Lnk1e in /opt/gaussian/g03/l301.exe at Fri Mar 14 20:01:07 2008. > > Please could anyone help me to solve this problem ? > > Thank you very much for your help. > > Best wishes. > Pavlina KOSINOVA > (Ph.D. student)> From owner-chemistry@ccl.net Thu Mar 27 08:53:01 2008 From: "Wolf-D. Ihlenfeldt wdi===xemistry.com" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36563-080327070846-27607-J9pkSqFr45Mr7lNj4nZb3g---server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Thu, 27 Mar 2008 11:04:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi{:}xemistry.com] Junjun, Standard fast 2D algorithms compute a set of fingerprints (lots of = literature can be found about which fingerprint performs best under = different circumstances) from the molecules and compare them by some = function (standard methods are Tanimoto and Tversky, but there are quite = a few other suitable functions). If you want a simple, but flexible and customizable solution, I = recommend Cactvs (free for academics, www.xemistry.com/academic) Sample script for the Tanimoto score computation of two molecules = decoded from SMILES strings from the default substructure filtering = screen bit set: --- snip --- set e1 [ens create c1ncccc1] set e2 [ens create c1ncncc1] echo [prop compare E_SCREEN [ens get $e1 E_SCREEN] [ens get $e2 = E_SCREEN] tanimoto] --- Run with the standard interpreter from the package as "csts = -fmyscript.tcl" This will print a scaled integer between 0 and 100. (0.0 .. 1.0 score = multiplied to yield percentage) W. D. Ihlenfeldt Xemistry GmbH wdi-x-xemistry.com --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. = W. D. Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany HR Marburg B4713 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > -----Original Message----- > From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] > Sent: Wednesday, March 26, 2008 11:02 PM > To: Ihlenfeldt, Wolf D > Subject: CCL: similarity of different molecules >=20 >=20 > Sent to CCL by: "JunJun Liu" [ljjlp03\a/gmail.com] > Hello everybody, >=20 > I want to know how similar two different molecules are. Does anybody > know > how to do this? Any suggestions regarding algorithms or softwares are > highly appreciated! >=20 > Thanks in advance! >=20 > Junjun >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search) >=20>=20>=20 From owner-chemistry@ccl.net Thu Mar 27 09:26:00 2008 From: "Grace Y Tier Grace.Y.Tier/./usa.dupont.com" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36564-080327080616-8727-qY0HNHHi3ag+/7wZA+t/+w^-^server.ccl.net> X-Original-From: Grace Y Tier Content-Type: multipart/alternative; boundary="=_alternative 0042761C85257419_=" Date: Thu, 27 Mar 2008 08:05:55 -0400 MIME-Version: 1.0 Sent to CCL by: Grace Y Tier [Grace.Y.Tier ~ usa.dupont.com] This is a multipart message in MIME format. --=_alternative 0042761C85257419_= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Hi Junjun, If you are interested in exploring the similarity of two substances with respect to their toxicity through using a range of different similarity indices then you might wish to try the following program Toxmatch. It is open source and freely available from the European Chemicals Bureau website. See http://ecb.jrc.it/qsar/qsar-tools/index.php?c=TOXMATCH for more information and download instructions. Grace "JunJun Liu ljjlp03]~[gmail.com" Sent by: owner-chemistry||ccl.net 03/26/2008 08:13 PM Please respond to "CCL Subscribers" To Grace Y Tier/AE/DuPont||DuPont cc 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 how to do this? Any suggestions regarding algorithms or softwares are highly appreciated! Thanks in advance! Junjunhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html --=_alternative 0042761C85257419_= Content-Transfer-Encoding: 7bit Content-Type: text/html; charset="us-ascii"
Hi Junjun,

If you are interested in exploring the similarity of two substances with respect to their toxicity through using a range of different similarity indices then you might wish to try the following program Toxmatch. It is open source and freely available from the European Chemicals Bureau website. See http://ecb.jrc.it/qsar/qsar-tools/index.php?c=TOXMATCH for more information and download instructions.

Grace

"JunJun Liu ljjlp03]~[gmail.com" <owner-chemistry||ccl.net>
Sent by: owner-chemistry||ccl.net

03/26/2008 08:13 PM

Please respond to
"CCL Subscribers" <chemistry||ccl.net>

To	Grace Y Tier/AE/DuPont\|\|DuPont
cc
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 how to do this? Any suggestions regarding algorithms or softwares are highly appreciated! Thanks in advance! Junjun http://www.ccl.net/cgi-bin/ccl/send_ccl_message http://www.ccl.net/cgi-bin/ccl/send_ccl_message http://www.ccl.net/chemistry/sub_unsub.shtml Search Messages: http://www.ccl.net/htdig (login: ccl, Password: search) http://www.ccl.net/spammers.txt

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--=_alternative 0042761C85257419_=-- From owner-chemistry@ccl.net Thu Mar 27 16:44:00 2008 From: "aa aa!^!chemaxon.hu" To: CCL Subject: CCL: ChemAxon's European User Group Meeting - 7-8 May, Visegrad, Hungary - Program announcement and call for participants Message-Id: <-36565-080327164208-21327-DyARyF9wu2A/rYqfyJCU/A*_*server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------050808020607020203030705" Date: Thu, 27 Mar 2008 16:41:52 -0400 MIME-Version: 1.0 Sent to CCL by: aa [aa[#]chemaxon.hu] This is a multi-part message in MIME format. --------------050808020607020203030705 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Good day, The program is now available for ChemAxon's 2008 European User Group Meeting being held on Wednesday and Thursday, May 7-8th at the Thermal Hotel Spa in Visegrad, Hungary. The meeting will preceded by a workshop and training day on May 6th. The meeting will feature presentations from ChemAxon users, a lightning presentation session and exhibition from ChemAxon Partners and the latest updates on product developments. Preceding the meeting will be a 2 track workshop and training day for both end users and developers. As usual we will have extensive social events for attendees to mix and enjoy. To find out more about the meeting, register or submit a poster abstract (open until April 15th) and view the program, please visit: http://www.chemaxon.com/UGM/08/index.html. To find out more about the topics for the training and workshop day please visit: http://www.chemaxon.com/training/0508.html See you there. Alex Confirmed speakers include: P�ter V�rkonyi, Astra Zeneca R&D Davide Audisio, Aureus Pharma Dragos Horvath, CNRS Catherine Reisser, Evotec Alistair Sedwell, Evotec Wayne Mitchell, Experiment Research Centre, Singapore Shunichi Ozawa, Infocom Lutz Weber, OntoChem Eszter Hazai, Virtua Drug ChemAxon Partners (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html -- Alex Allardyce Dir. Marketing, ChemAxon --------------050808020607020203030705 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Good day,

The program is now available for ChemAxon's 2008 European User Group Meeting being held on Wednesday and Thursday, May 7-8th at the Thermal Hotel Spa in Visegrad, Hungary. The meeting will preceded by a workshop and training day on May 6th.

The meeting will feature presentations from ChemAxon users, a lightning presentation session and exhibition from ChemAxon Partners and the latest updates on product developments. Preceding the meeting will be a 2 track workshop and training day for both end users and developers. As usual we will have extensive social events for attendees to mix and enjoy.

To find out more about the meeting, register or submit a poster abstract (open until April 15th) and view the program, please visit: http://www.chemaxon.com/UGM/08/index.html.

To find out more about the topics for the training and workshop day please visit: http://www.chemaxon.com/training/0508.html

See you there.
Alex

Confirmed speakers include:
Péter Várkonyi, Astra Zeneca R&D
Davide Audisio, Aureus Pharma
Dragos Horvath, CNRS
Catherine Reisser, Evotec
Alistair Sedwell, Evotec
Wayne Mitchell, Experiment Research Centre, Singapore
Shunichi Ozawa, Infocom
Lutz Weber, OntoChem
Eszter Hazai, Virtua Drug
ChemAxon Partners (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html

--
Alex Allardyce
Dir. Marketing, ChemAxon --------------050808020607020203030705-- From owner-chemistry@ccl.net Thu Mar 27 21:47:00 2008 From: "Hongqing He leohhq\a/sohu.com" To: CCL Subject: CCL: Need your help about " RESTARTED DUE TO LINMIN FAILURE ". Message-Id: <-36566-080327202144-32685-YlFieNXJrc2T5kex/YFVSw() server.ccl.net> X-Original-From: "Hongqing He" Date: Thu, 27 Mar 2008 20:21:40 -0400 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