From chemistry-request@ccl.net Wed Oct 8 02:48:38 2003 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h986m659019064 for ; Wed, 8 Oct 2003 02:48:07 -0400 Received: from dmbr032.fvms.ugent.be (dmbr032.fvms.ugent.be [157.193.200.89]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 23DBE68004; Wed, 8 Oct 2003 08:48:06 +0200 (CEST) Subject: Re: CCL:Atomic contact energies From: Dominique Vlieghe To: Craig Shepherd Cc: forum CCL In-Reply-To: <3F821F45.5000300*at*scripps.edu> References: <3F821F45.5000300*at*scripps.edu> Content-Type: text/plain Organization: Message-Id: <1065595536.4015.11.camel*at*dmbr032.fvms.ugent.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 08 Oct 2003 08:45:36 +0200 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-4.9 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_XIMIAN version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Craig, hi rest, On Tue, 2003-10-07 at 04:04, Craig Shepherd wrote: > Hello all, > > Does anyone know of a program (standalone or incorporated into some > package) that will calculate atomic contact energies (ACE) for a protein > structure(s)? > It seems that a lot of docking groups use them in their scoring > functions, so my > hunch is the programs are out there. > I asked Rong Chen - the author of ZDOCK and RDOCK - practically the same question some time ago (but related to protein-protein docking), and this is an excerpt of his reply: ... To calculate ACE energy, you just divide all protein atoms into 18 atom types, count the number of i-j atom pairs within 6 angstrom. Each i-j atom pair gets an ACE score of deltaG(ij). Sum over all i-j pairs, you will get the ACE energy for the protein complex. There is a program called mark_sur.f in ZDOCK package to mark ACE types for all protein atoms according to uniCHARMM, which is a parameter file included in ZDOCK release. After marking ACE types for all atoms using mark_sur.f, you can easily write a script to count the number of i-j atom pairs, and sum over i and j to get the ACE energy for the whole complex... Of course, what he is saying is basically: DIY :-) So if someone knows of such a ACE calculating tool, I'm also very interested Regards, Dominique > So you know what I'm talking about, the ACE's I'm talking about are > described in > the following references: > > Miyazawa, S. and Jernigan, R.L. Estimation of effective interresidue > contact energies from > protein crystal structures: quasi-chemical approximation. 1985. > /Macromolecules/ 18:534-552. > > Zhang, C. /et al. /Determinations of atomic desolvation energies from > the structures of crystallized > proteins. 1997. /J. Mol. Biol. /267:707-726. > > Thanks a lot, > > Craig Shepherd > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl*at*ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University (new) 'Fiers-Schell-Van Montagu' building (new) Technologiepark 927 (new) B-9052 Ghent (Zwijnaarde), Belgium (new) Tel : +32-(0)9-33-13.693 (new) Fax : +32-(0)9-33-13.609 (new) email:dominique.vlieghe*at*dmbr.ugent.be (new) www:http://www.dmbr.ugent.be/ ------------------------------ From chemistry-request@ccl.net Wed Oct 8 02:23:36 2003 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h986N459018466 for ; Wed, 8 Oct 2003 02:23:05 -0400 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h986g8c03855 for ; Wed, 8 Oct 2003 14:42:16 +0800 Date: Wed, 8 Oct 2003 14:42:08 +0800 (HKT) From: Hu LiHong To: chemistry/at/ccl.net Subject: CHARMM question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I am calculating protein by QMMM in standalone CHARMM. There is a warning "NBFIX involves an atom in a vdw group; Whole VDW group modified" because of one element "BR", did you encounter this problem? Could anyone tell me the reason and how to solve it? Thank you for your any comment, Best Carol From chemistry-request@ccl.net Tue Oct 7 19:24:32 2003 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h97NO159010505 for ; Tue, 7 Oct 2003 19:24:01 -0400 Received: from hymn10.u.washington.edu (hymn10.u.washington.edu [140.142.15.132]) by mxout4.cac.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h97NNqmw026514 for ; Tue, 7 Oct 2003 16:23:53 -0700 Received: from localhost (localhost [127.0.0.1]) by hymn10.u.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h97NNqRY019084 for ; Tue, 7 Oct 2003 16:23:52 -0700 Date: Tue, 7 Oct 2003 16:23:52 -0700 (PDT) From: "James P. Sullivan" To: chemistry$at$ccl.net Subject: CHARMM on Linux Emulator Message-ID: Received: from [140.142.15.150] by hymn10.u.washington.edu via HTTP; Tue, 07 Oct 2003 16:23:52 PDT MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII X-Spam-Status: No, hits=0.4 required=7.0 tests=MSG_ID_ADDED_BY_MTA_2,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Has anyone successfully installed and run CHARMM on a linux emulator such as: http://bochs.sourceforge.net Boch is an emulator of Linux. http://plex86.sourceforge.net The free version of VMWare is Plex86. http://www.cygwin.com We would like to be able to run charmm jobs on PCs in our group. Thanks, Jim Sullivan PhD student in Chemical Engineering University of Washington From chemistry-request@ccl.net Wed Oct 8 09:44:31 2003 Received: from zmail.pt ([213.13.155.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h98Dhx59031485 for ; Wed, 8 Oct 2003 09:43:59 -0400 Received: from WorldClient (authenticated user goncalo.justino~at~zmail.pt) by zmail.pt (MDaemon.PRO.v6.8.4.R) with ESMTP id 59-md50000000013.tmp for ; Wed, 08 Oct 2003 14:40:49 +0100 Received: from [194.117.40.12] via WorldClient with HTTP; Wed, 08 Oct 2003 14:40:48 +0100 Date: Wed, 08 Oct 2003 14:40:48 +0100 From: "=?iso-8859-1?Q?Gon=E7alo?= Deira Justino" To: CHEMISTRY~at~ccl.net Subject: CCL: AM1, MNDO and PM3 - Summary MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Message-ID: X-Mailer: ZMAIL.PT 6.8.4 X-Authenticated-Sender: goncalo.justino~at~zmail.pt X-Spam-Processed: mx1-carrier, Wed, 08 Oct 2003 14:40:49 +0100 (not processed: spam filter disabled) X-Return-Path: goncalo.justino~at~zmail.pt X-MDaemon-Deliver-To: CHEMISTRY~at~ccl.net Reply-To: goncalo.justino~at~zmail.pt X-Spam-Status: No, hits=0.4 required=7.0 tests=NO_COST,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Here goes a summary of all replies to my question on AM1, PM3 and MNDO. Thanks 2u all Gongalo === I am sending attached to this e-mail a windows compiled version of the mopac6 program and its manual. Even when mopac is not longer free, this version is still aviable at no cost. This compilation is quite similar to the original (some improvements made for the pentium processor) and should work fine. If you are unabled to recieved please let me know and something could be done. A comertial option could be the Hyperchem program, althought is quite expensive and not-so-good as the good old mopac. By the way, mopac could be used in conjuntion with Vega or even Rasmol to review the results, and using Babel you can convert the mopac format to almost any readable by your favorite modeling program. Best Regards, Juan Alexander Padron-Garcia, PhD Student. === Try MOPAC2002. It has MONDO-d and PM5 also. Istvan === Depending on your OS, there are several incarnations of MOPAC available. Most are built on MOPAC 6, which is a wonderfully stable code. Personally, I use an older version of MacSpartan from Wavefunction (this is on a Mac G3 with Mac OS 9), with some work being done in WinMopac. For Windows, look at WinMopac, which is available free on the Web. For Linux/UNIX, there are too many to count, altogether too many of which have been tinkered with. If you have compilers and all, I would recommend getting a virgin copy from CCL or QCPE, and building your own executable ... you get the manual that way, too! If you are not a developer, resist the temptation to use MOPAC 7, which was not intended as a production version. Getting entropy and stuff in MOPAC involves doing a very rigorous geometry optimization, then a force and thermodynamics calculation. This can all be done in the same run, with the correct selection of keywords, and paging through the voluminous output. Hope this helps, Steve === oops, WinMopac is used by at least two ortganizations. The free version is WinMopac 7.2.1, which is a Mopac 7 variant (so much for my warning!). At least one other "WinMopac" is or was available > from Fujitsu/Cache. Note that Jimmy Stewart works for Fujitsu, and so these are probably blessed versions. But also commercial ... sb === think by far the most stable and mature program is GAMESS-US, which includes semiempirical methods like AM1, PM3 and MNDO. One advantage is that GAMESS is also a higher-level program which includes HF, MP2 and DFT methods (among other) if you want higher accuracy optimizations. GAMESS is free, but not public domain: http://www.msg.ameslab.gov/GAMESS/dist.menu.html Cheers, -Geoff === ArgusLab is a Windows-based modeling program that has a non-MOPAC implementation of MNDO, AM1, and PM3. Also, ArgusLab v4.0 has a Gaussian interface that gives you easy access to Gaussian's implementations of those methods. ArgusLab 3.1 is free for academic faculty and students. ArgusLab 4.0 is now in beta release if you'd like to try it out. Both can be obtained at: http://www.arguslab.com Mark === > Dear CCL, > > I'm currently using AM1, MNDO and PM3 methods to optimize > molecular geometries. Can you tell me any software, > preferentially free, but not only, that does this? If it also > allows me to get entropy and related stuff, it'd be cool. > > Thanks ____________________________________ Gongalo Deira Campos Justino Theoretical&Antioxidant Biochemistry PhD student~at~www.dqb.fc.ul.pt goncalo.justino~at~zmail.pt ____________________________________ "Let your mind be free" From chemistry-request@ccl.net Wed Oct 8 11:57:22 2003 Received: from sgofims02.ccs.ppg.com (smtpout.ppg.com [141.189.251.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h98Fuldm003398 for ; Wed, 8 Oct 2003 11:56:47 -0400 Received: by sgofims02.ccs.ppg.com with Internet Mail Service (5.5.2653.19) id <41RBD291>; Wed, 8 Oct 2003 11:56:38 -0400 Message-ID: <3251EC702A37B9458A01D917C3D3B389034FFA_at_sgofusr20.nac.ppg.com> From: "Deng, Jun" To: "'chemistry_at_ccl.net'" Subject: explanation of excited state calculation Date: Wed, 8 Oct 2003 11:56:33 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear college: I am having a hard time to rationalize the vertical excited state calculation. Here are two examples from TDDFT calculation. The first example shows the first singlet excited state is at 519 nm with intensity of 0.8344 and it is from HOMO -> LUMO, which makes sense to me. However, in the 2nd example, the major contribution of first several excited states are not from HOMO->LUMO any more and their intensity are very low, what is causing this? How to rationalize that the lowest absorption band is not from HOMO->Lumo in example 2? How to explain their low intensity? Thank you very much in advance! Jun Deng Example 1: ------------------ ..... Excitation energies and oscillator strengths: CIS wavefunction symmetry could not be determined. Excited State 1: Singlet-?Sym 2.3877 eV 519.25 nm f=0.8344 111 ->112 0.60683 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. CIS wavefunction symmetry could not be determined. Excited State 2: Singlet-?Sym 2.7187 eV 456.04 nm f=0.0143 109 ->112 0.66284 110 ->112 0.15775 CIS wavefunction symmetry could not be determined. Excited State 3: Singlet-?Sym 2.9144 eV 425.41 nm f=0.1573 108 ->112 0.10820 109 ->112 -0.15727 110 ->112 0.64066 ********************************************************************** Example 2: ---------------- ... Excitation energies and oscillator strengths: CIS wavefunction symmetry could not be determined. Excited State 1: Singlet-?Sym 1.8767 eV 660.63 nm f=0.0018 108 ->115 -0.11035 108 ->116 0.20162 109 ->111 0.51094 109 ->112 -0.11881 109 ->115 -0.31646 109 ->116 -0.12306 109 ->117 -0.14693 110 ->116 0.14532 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. CIS wavefunction symmetry could not be determined. Excited State 2: Singlet-?Sym 1.9109 eV 648.81 nm f=0.0440 108 ->111 0.36507 108 ->112 -0.10467 108 ->115 -0.27320 108 ->116 -0.10897 108 ->117 -0.13976 109 ->111 -0.11460 109 ->115 0.13735 109 ->116 -0.25594 110 ->111 0.30348 110 ->115 -0.17043 CIS wavefunction symmetry could not be determined. Excited State 3: Singlet-?Sym 2.3975 eV 517.14 nm f=0.0985 105 ->111 0.18235 105 ->115 -0.22021 105 ->117 -0.11614 108 ->116 0.13778 109 ->114 -0.11851 109 ->115 -0.12217 109 ->116 0.43242 110 ->111 0.28462 CIS wavefunction symmetry could not be determined. Excited State 4: Singlet-?Sym 2.4312 eV 509.97 nm f=0.0116 105 ->116 0.17280 108 ->114 0.11007 108 ->115 0.13363 108 ->116 -0.39502 109 ->111 0.32852 109 ->115 0.10826 109 ->116 0.17199 109 ->117 0.10013 110 ->111 0.11137 110 ->116 -0.25594 CIS wavefunction symmetry could not be determined. Excited State 5: Singlet-?Sym 2.5613 eV 484.07 nm f=0.3805 105 ->111 -0.12691 105 ->115 0.17900 107 ->111 0.16390 108 ->111 -0.30706 109 ->116 -0.13230 110 ->111 0.42057 CIS wavefunction symmetry could not be determined. Excited State 6: Singlet-?Sym 2.6477 eV 468.27 nm f=0.0142 105 ->111 -0.22953 105 ->115 0.22375 105 ->117 0.11472 106 ->111 -0.12855 108 ->111 0.44043 108 ->115 0.18104 108 ->117 0.12017 109 ->115 -0.10034 110 ->115 0.18972 110 ->117 0.10481 ********************************************************************** From chemistry-request@ccl.net Wed Oct 8 11:15:58 2003 Received: from kdmail2.netcologne.de (kdmail2.netcologne.de [194.8.194.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h98FFP59002425 for ; Wed, 8 Oct 2003 11:15:26 -0400 Received: from cosmologic.de (xdsl-213-168-119-104.netcologne.de [213.168.119.104]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id AAV58510 (AUTH klamt:at:cosmologic.de); Wed, 8 Oct 2003 17:09:43 +0200 (CEST) Message-ID: <3F842899.6050207:at:cosmologic.de> Date: Wed, 08 Oct 2003 17:09:13 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry:at:ccl.net" Subject: Re: CCL:Atomic contact energies References: <3F821F45.5000300:at:scripps.edu> <1065595536.4015.11.camel:at:dmbr032.fvms.ugent.be> Content-Type: multipart/alternative; boundary="------------030700010302090707010907" X-Spam-Status: No, hits=0.4 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_10_20,HTML_MESSAGE,REFERENCES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --------------030700010302090707010907 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Just a thought regarding ACEs: My COSMO-RS solvation model describes the free energy of molecules in the liquid phase by pairwise interactions of surfaces. But it makes use of surface polarization charge densities (sigma) of both surface segments, which result DFT/COSMO calculations. In case one should not be able to afford such calculations for the purpose you have in mind, you get approximate polarization charge densities from similar regions of molecules. We have a tool COSMOfrag to do so. Thus in the end you would be able to get an estimate of the entire interaction energies (and can simply subtract the desolvation free energy within the COSMO-RS theory). Even with the approximate sigma's this scheme should be more robust than just atom contact energies. Please see our homepage for more information and references on COSMO-RS, and contact me for a eventual collaboration on the development of such scoring tool. Regards Andreas Dominique Vlieghe wrote: >Hi Craig, hi rest, > >On Tue, 2003-10-07 at 04:04, Craig Shepherd wrote: > > >>Hello all, >> >>Does anyone know of a program (standalone or incorporated into some >>package) that will calculate atomic contact energies (ACE) for a protein >>structure(s)? >>It seems that a lot of docking groups use them in their scoring >>functions, so my >>hunch is the programs are out there. >> >> >> > >I asked Rong Chen - the author of ZDOCK and RDOCK - practically the same >question some time ago (but related to protein-protein docking), and >this is an excerpt of his reply: > > > > >>... To calculate ACE energy, you just divide all protein atoms into 18 >> >> >atom types, count the number of i-j atom pairs within 6 angstrom. Each >i-j atom pair gets an ACE score of deltaG(ij). Sum over all i-j pairs, >you will get the ACE energy for the protein complex. There is a program >called mark_sur.f in ZDOCK package to mark ACE types for all protein >atoms according to uniCHARMM, which is a parameter file included in >ZDOCK release. After marking ACE types for all atoms using mark_sur.f, >you can easily write a script to count the number of i-j atom pairs, and >sum over i and j to get the ACE energy for the whole complex... > >Of course, what he is saying is basically: DIY :-) So if someone knows >of such a ACE calculating tool, I'm also very interested > >Regards, > >Dominique > > > > >>So you know what I'm talking about, the ACE's I'm talking about are >>described in >>the following references: >> >>Miyazawa, S. and Jernigan, R.L. Estimation of effective interresidue >>contact energies from >>protein crystal structures: quasi-chemical approximation. 1985. >>/Macromolecules/ 18:534-552. >> >>Zhang, C. /et al. /Determinations of atomic desolvation energies from >>the structures of crystallized >>proteins. 1997. /J. Mol. Biol. /267:707-726. >> >>Thanks a lot, >> >>Craig Shepherd >> >> >> >> >> >> >>HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs >> >> >> >> >> -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt:at:cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- --------------030700010302090707010907 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Just a thought regarding ACEs:
My COSMO-RS solvation model describes the free energy of molecules in the liquid phase by pairwise interactions of surfaces. But it makes use of surface polarization charge densities (sigma) of both surface segments, which result DFT/COSMO calculations. In case one should not be able to afford such calculations for the purpose you have in mind, you get approximate polarization charge densities from similar regions of molecules. We have a tool COSMOfrag to do so. Thus in the end you would be able to get an estimate of the entire interaction energies (and can simply subtract the desolvation free energy within the COSMO-RS theory). Even with the approximate sigma's this scheme should be more robust than just atom contact energies.

Please see our homepage for more information and references on COSMO-RS, and contact me for a eventual collaboration on the development of such scoring tool.

Regards

Andreas

Dominique Vlieghe wrote:
Hi Craig, hi rest,

On Tue, 2003-10-07 at 04:04, Craig Shepherd wrote:
  
Hello all,

Does anyone know of a program (standalone or incorporated into some
package) that will calculate atomic contact energies (ACE) for a protein 
structure(s)?
It seems that a lot of docking groups use them in their scoring 
functions, so my
hunch is the programs are out there.

    

I asked Rong Chen - the author of ZDOCK and RDOCK - practically the same
question some time ago (but related to protein-protein docking), and
this is an excerpt of his reply:


  
... To calculate ACE energy, you just divide all protein atoms into 18
    
atom types, count the number of i-j atom pairs within 6 angstrom. Each
i-j atom pair gets an ACE score of deltaG(ij). Sum over all i-j pairs,
you will get the ACE energy for the protein complex. There is a program
called mark_sur.f in ZDOCK package to mark ACE types for all protein
atoms according to uniCHARMM, which is a parameter file included in
ZDOCK release. After marking ACE types for all atoms using mark_sur.f,
you can easily write a script to count the number of i-j atom pairs, and
sum over i and j to get the ACE energy for the whole complex...

Of course, what he is saying is basically: DIY :-)  So if someone knows
of such a ACE calculating tool, I'm also very interested

Regards,

Dominique


  
So you know what I'm talking about, the ACE's I'm talking about are 
described in
the following references:

Miyazawa, S. and Jernigan, R.L. Estimation of effective interresidue 
contact energies from
protein crystal structures: quasi-chemical approximation.  1985.  
/Macromolecules/ 18:534-552.

Zhang, C. /et al. /Determinations of atomic desolvation energies from 
the structures of crystallized
proteins. 1997.  /J. Mol. Biol. /267:707-726.

Thanks a lot,

Craig Shepherd






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        Computational Chemistry and Fluid Thermodynamics
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--------------030700010302090707010907-- From chemistry-request@ccl.net Wed Oct 8 13:33:44 2003 Received: from antivirus2.its.rochester.edu (antivirus2.its.rochester.edu [128.151.57.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h98HX9dm006434 for ; Wed, 8 Oct 2003 13:33:11 -0400 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h98HX3EK006532 for ; Wed, 8 Oct 2003 13:33:04 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with SMTP id h98HWsnJ006484 for ; Wed, 8 Oct 2003 13:32:54 -0400 (EDT) Received: from mail.rochester.edu (mail.rochester.edu [128.151.224.17]) by mail.rochester.edu (8.12.4/8.12.1) with SMTP id h98HWshI029746 for ; Wed, 8 Oct 2003 13:32:54 -0400 (EDT) Sender: weiz[at]mail.rochester.edu From: "weiz" Reply-to: weiz[at]mail.rochester.edu To: chemistry[at]ccl.net Subject: a question about Hydrogen bonding criteria in peptide simulation X-Mailer: Quality Web Email v3.0q, http://netwinsite.com/refw.htm Date: Wed, 08 Oct 2003 13:32:54 -0400 Priority: normal Message-id: <3f844a46.7431.4633[at]mail.rochester.edu> X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear colleagues: I know that there are two kinds of criterias of judging the existance of the hydrogen bond in peptide simulation. one is geometry criteria,another is energy criteria. can any one give me some importance reference about using these criterias.also , comments about the each kind are very welcome too. wei From chemistry-request@ccl.net Wed Oct 8 20:03:59 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9903Ndm016090 for ; Wed, 8 Oct 2003 20:03:27 -0400 Received: (eyou send program); Thu, 09 Oct 2003 08:04:07 +0800 Received: from unknown (HELO qiang) (unknown@128.195.173.219) by 202.113.16.21 with SMTP; Thu, 09 Oct 2003 08:04:07 +0800 Date: Wed, 8 Oct 2003 17:03:09 -0700 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <388923819.20031008170309!at!joyie.com> To: "chemistry!at!ccl.net" Subject: GDIIS and Z-MATRIX MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, Z-matrix optimization only work with Berny algorithm. What if I have to use GDIIS and still want to control the zmatrix symmetry. Is there a way to do it? -- Best regards, John