From owner-chemistry@ccl.net Tue Sep 18 01:00:00 2007 From: "Satyan Sharma satyan++sun3.oulu.fi" To: CCL Subject: CCL:G: Crashing IRC : Further info Message-Id: <-35187-070918005850-10551-OuRVGla+UnjWOzBfzWcJqQ{:}server.ccl.net> X-Original-From: "Satyan Sharma" Date: Tue, 18 Sep 2007 00:58:47 -0400 Sent to CCL by: "Satyan Sharma" [satyan]=[sun3.oulu.fi] Dear CClers, I am studying an enzyme phospotransfer reaction. Taking a few residues from the active site, I have found the Transition state guess using partial PES scan using gaussian03. The TS was optimized using N B3lyp/6-31G* OPT=(TS,CalcFc,NoEigen) NOSYMM TEST The TS was confirmed using route: N B3LYP/6-31G* Freq NoSymm Test Here is output from Freq: Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- -158.6525 16.8447 20.1106 Red. masses -- 14.3275 5.8131 7.0497 After obtaining a single -ve freq, planned to do IRC. I used the following in the route section. N B3LYP/6-31G* IRC(RCFC,Forward) NoSymm Test The Calculation crashes in the very first step. * Output from IRC: Z66 0.00104 0.00073 0.00160 -0.00034 -0.00076 X66 Y66 Z66 X66 0.28938 Y66 -0.07623 0.04939 Z66 -0.11068 0.04111 0.11344 ANGLE THETA= 93.10860 BRACKET FOR LAMBDA OBTAINED IN CYCLES= 99 Arithmetic Exception real 33:52.86 user 2:14:30.35 sys 31.52 Any suggestions are appreciated. Regards, Satyan From owner-chemistry@ccl.net Tue Sep 18 02:35:01 2007 From: "Orlin Blajiev blajiev() vub.ac.be" To: CCL Subject: CCL:G: Density Message-Id: <-35188-070917104031-18756-er1nFeQgxQ3KBxsq40Lppg:_:server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Sep 2007 16:08:23 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev|vub.ac.be] Hi everybody, I have a question about the following. I calculate something with ONIOM with Gaussian and when I try to turn the formatted checkpoint to cube I am getting an error message that Density is not found in the file. When I do not use ONIOM everything is OK. Does somebody have an idea what is wrong? Best regards, Orlin -- Orlin Blajiev Materials and Chemistry (MACH) Dept. Metallurgy, Electrochemistry and Materials Science (META) Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev,+,vub.ac.be http://www.vub.ac.be/META From owner-chemistry@ccl.net Tue Sep 18 06:14:00 2007 From: "Julien Lefeuvre j.lefeuvre(-)iecb.u-bordeaux.fr" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35189-070918061252-24004-/7BjtPAmPZ+aWRFAFqwNAQ||server.ccl.net> X-Original-From: Julien Lefeuvre Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 18 Sep 2007 12:12:31 +0200 MIME-Version: 1.0 Sent to CCL by: Julien Lefeuvre [j.lefeuvre|*|iecb.u-bordeaux.fr] Jerome Kieffer jerome.Kieffer]|[terre-adelie.org wrote: > Sent to CCL by: Jerome Kieffer [jerome.Kieffer{:}terre-adelie.org] > On Mon, 17 Sep 2007 10:58:29 +0200 > "Julien Lefeuvre j.lefeuvre%x%iecb.u-bordeaux.fr" > wrote: > >> I know 3 open source software able to convert SMILES code to flat 2D >> representation: >> bkckem >> xdrawchem >> and of course openbabel > > I know babel and openbabel for half a dozen year now and I wonder how > to convert a smiles into a 2D or a 3D because I got all coordinate to > zero. My bad, you are right. I have always used openbabel smiles capabilities to generate 3D. I bypassed this problem by generating some random coordinates for each atom and minimising the energy then after ... This is what happen when one is replying too fast. For your conversion from smiles to isis (provided that isis is able to import CML or molfile format), bkchem should be interesting. HIH Julien Lefeuvre -- Getting the job done is no excuse for not following the rules. Corollary: Following the rules will not get the job done. From owner-chemistry@ccl.net Tue Sep 18 06:49:01 2007 From: "Sina T reli sinatureli\a/gmail.com" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35190-070918062258-28039-f/yADe7xi0JBjyOD3bd2vw[]server.ccl.net> X-Original-From: "Sina T reli" Date: Tue, 18 Sep 2007 06:22:53 -0400 Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com] Hello, I have a few questions regarding hyperchem. From owner-chemistry@ccl.net Tue Sep 18 08:48:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli+/-gmail.com" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35191-070918081845-28723-g4o7he2DueXu++LGDBCL2w===server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_5597_21787909.1190116321340" Date: Tue, 18 Sep 2007 14:52:01 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli-*-gmail.com] ------=_Part_5597_21787909.1190116321340 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hmm for some reasons my questions did not appear... So I will post them here When I do geometry optimization with mndo/d on a biomolecule after some time some of the atoms bond to each other while doing the same optimization in spartan with am1 or pm3 does not yield such results. What may be the cause of this, and how can I prevent that? And also when I try to run mopac from hyperchem, it opens the input file but then it gives a "program teriminated with exit code 0" error.. What may be the cause of this? Thanks.. On 9/18/07, Sina T reli sinaturelia/gmail.com wrote: > > > Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com] > Hello, > > I have a few questions regarding hyperchem.> > > > ------=_Part_5597_21787909.1190116321340 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hmm for some reasons my questions did not appear... So I will post them here

When I do geometry optimization with mndo/d on a biomolecule after some time some of the atoms bond to each other while doing the same optimization in spartan with am1 or pm3 does not yield such results. What may be the cause of this, and how can I prevent that?

And also when I try to run mopac from hyperchem, it opens the input file but then it gives a "program teriminated with exit code 0"
error.. What may be the cause of this?

Thanks..


On 9/18/07, Sina T reli sinaturelia/gmail.com <owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinatureli]![gmail.com]
Hello,

I have a few questions regarding hyperchem.



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------=_Part_5597_21787909.1190116321340-- From owner-chemistry@ccl.net Tue Sep 18 09:22:00 2007 From: "Daniel Jana dfjana-*-gmail.com" To: CCL Subject: CCL:G: gaussian Message-Id: <-35192-070918085444-1762-klLzgQ8t/R86nwJL4UpC3w*_*server.ccl.net> X-Original-From: "Daniel Jana" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 18 Sep 2007 13:54:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Daniel Jana" [dfjana:-:gmail.com] On 17/09/2007, pragya chohan pragyachohan],[hotmail.com wrote: > > Sent to CCL by: "pragya chohan" [pragyachohan!^!hotmail.com] > hi.. i m getting the following error... i guess it is because of lack of memory.... is it really so.... pls help > Out-of-memory error in routine After all major allocation (IEnd= 1229340 MxCore= 969022) > Use %mem=7MW to provide the minimum amount of memory required to complete this step. > Error termination via Lnk1e in /nepdisk11/g03/l502.exe at Mon Sep 17 20:59:14 2007. Hello, Yes, it seems to be due to the small amount of memory you have for that job. You should use a %mem line with a number equal or higher to 7MW (or equivalent in bytes, which is 8 times higher). Daniel PS - Did you at least try to increase the memory before asking here? Learning is made and problems are solved, first through thinking and only after that through asking questions. The error message was pretty clear! From owner-chemistry@ccl.net Tue Sep 18 10:00:01 2007 From: "Debellis Anthony CE US anthony.debellis-*-cibasc.com" To: CCL Subject: CCL:G: GAUSSIAN-basis sets Message-Id: <-35193-070918094429-31978-DKwUDmLUpsr5uDvFVFM7BQ/./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: Tue, 18 Sep 2007 09:12:30 -0400 MIME-Version: 1.0 Sent to CCL by: Debellis Anthony CE US [anthony.debellis ~~ cibasc.com] Julie, You should consult the Gaussian manual under the keywords GEN, GENECP, and PSEUDO. The use of mixed basis sets is explained there. Anthony=20 -----Original Message----- > From: owner-chemistry..ccl.net [mailto:owner-chemistry..ccl.net]=20 Sent: Monday, September 17, 2007 9:07 PM To: Debellis Anthony CE US Subject: CCL:G: GAUSSIAN-basis sets Sent to CCL by: "Julie H Hwang" [jhwang5=3D-=3Dmail.rochester.edu] Dear = all, Hi I have a question on choosing basis set(s). I want to calculate Raman spectra peaks for ferrocene and I was wondering if I can choose different basis sets for non-metals (C and H) and metal (Fe). I tried to look up the Gaussian manual, but they didn't specify the availability of such option. Thank you for your time! -=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 Tue Sep 18 10:33:01 2007 From: "Herbert Fruchtl herbert.fruchtl:+:st-andrews.ac.uk" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35194-070918095044-2419-/5skQuMtzqQRhsvn7AvhcQ/a\server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Sep 2007 14:50:11 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl^-^st-andrews.ac.uk] I don't use Hyperchem or Spartan, but... AM1 and PM3 are Hamiltonians, so any program that implements them should give the same single-point energy and gradient (bar some numerical noise). The geometry optimization algorithm uses these numbers to find a minimum on the potential energy surface. This algorithm is not part of the method, and different programs may find different minima. If you want a specific one (i.e. you know roughly what the result should look like), you have to start at a geometry close to the correct result (whatever "close" means in this context; something like "not separated by an energy barrier"). For most programs and operating systems, "exit code 0" means normal termination. If that happens immediately, MOPAC either didn't find the input, detected an error in the input, or found another reason why it couldn't run (e.g. not enough memory, etc.). It should have created output files (*.log, *.out and/or *.arc). Unless Hyperchem deletes those, you should find them and see if they give you a clue about what went wrong. HTH, Herbert Sina Türeli sinatureli+/-gmail.com wrote: > Hmm for some reasons my questions did not appear... So I will post them here > > When I do geometry optimization with mndo/d on a biomolecule after some > time some of the atoms bond to each other while doing the same > optimization in spartan with am1 or pm3 does not yield such results. > What may be the cause of this, and how can I prevent that? > > And also when I try to run mopac from hyperchem, it opens the input file > but then it gives a "program teriminated with exit code 0" > error.. What may be the cause of this? > > Thanks.. > > > On 9/18/07, *Sina T reli sinaturelia/gmail.com* > > wrote: > > > Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com > ] > Hello, > > I have a few questions regarding hyperchem. > > > > > > > > > E-mail to subscribers: CHEMISTRY+/-ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net > or use> > Search Messages: http://www.ccl.net/htdig > (login: ccl, Password: search)> > > > > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Tue Sep 18 14:43:00 2007 From: "training#molsoft.com andy#molsoft.com" To: CCL Subject: CCL: MolSoft ICM Workshop - "Protein Structure and Drug Discovery" Message-Id: <-35195-070917215959-31735-OAQXR8xtvmLjG3w+oUwkng a server.ccl.net> X-Original-From: "training]^[molsoft.com" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 17 Sep 2007 15:55:59 -0700 MIME-Version: 1.0 Sent to CCL by: "training###molsoft.com" [andy###molsoft.com] Thank you to everyone who contacted us about MolSoft's (www.molsoft.com) September workshop entitled "Protein Structure and Drug Discovery". The workshop is now completely full and has a waiting list. Due to the high demand for ICM training, we have scheduled our 2008 workshop dates. We expect these workshops to fill up as well, so please register as soon as possible to reserve your place at any of the following workshops: January 17th-18th, 2008 May 1st-2nd, 2008 (Coincides with the end of the CHI Drug Discovery Chemistry Conference in La Jolla) September 25th-26th, 2008 See www.molsoft.com/training.html for more information. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. All workshops are presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft) and occasional guest speakers. The workshops will consist of lectures, demonstrations and “hands-on” computational experiments and cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, chemical clustering, searching, superposition ... - QSAR, machine learning - Protein-Protein Docking We will showcase and train you in the use of many of our new developments in computational chemistry and biology including: - fully-flexible receptor-ligand docking - new structure and ligand based screening tools - automated model building into density - atomic property field chemical superposition - fast machine learning tools for QSAR - pharmacophore drawing and searching - compound library enumeration tools - screen-grabbing movie making “The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools.” Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy-$-molsoft.com or call (858)625 2000 ext.108. MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Tue Sep 18 15:20:00 2007 From: "Yubo Fan yubofan_+_mail.chem.tamu.edu" To: CCL Subject: CCL: polarizable force field in Amber 9 Message-Id: <-35196-070918140612-12513-/exqzl2CFLZEfT1eFxN/wA[]server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C7F9F4.C6D2F900" Date: Tue, 18 Sep 2007 13:06:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan a mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C7F9F4.C6D2F900 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, I am working on a urea-water system by using Amber 9. The MD simulations = have been working fine for both TIP3P and TIP4P models. But, when I = applied polarizable force field for the urea-TIP3P system, the Epolz = term (in the output file) goes weird. The values increase from -10100 to = 7900 for each 1-ns trajectory. The input file and leaprc files are shown = below: INPUT: oooooooooooooooooooooooooooooooooooooooo urea in water (7.626 M): 1 ns MD &cntrl imin =3D 0, irest =3D 1, ntx =3D 5, ntb =3D 1, ntp =3D 0, cut =3D 10, ntr =3D 0, ntc =3D 2, ntf =3D 2, tempi =3D 300.0, temp0 =3D 300.0, ntt =3D 3, gamma_ln =3D 1.0, nstlim =3D 500000, dt =3D 0.002, ntpr =3D 250, ntwx =3D 250, ntwr =3D 10000, nscm =3D 100, ioutfm =3D 1, iwrap=3D1, vlimit =3D 20.0, ipol =3D 1, / oooooooooooooooooooooooooooooooooooooooo LEAPRC: oooooooooooooooooooooooooooooooooooooooo logFile leap.log # # ----- leaprc for loading the 2002 pol. force field, no lone pairs # assumes that any unspecified nucleic acids are DNA=20 # # ----- leaprc for loading the modified mainchain torsion parameters # as described in # Wang et al, (2006) JCC, 27(6), 781-790 # # load atom type hybridizations # addAtomTypes { { "H" "H" "sp3" } { "HO" "H" "sp3" } { "HS" "H" "sp3" } { "H1" "H" "sp3" } { "H2" "H" "sp3" } { "H3" "H" "sp3" } { "H4" "H" "sp3" } { "H5" "H" "sp3" } { "HW" "H" "sp3" } { "HC" "H" "sp3" } { "HA" "H" "sp3" } { "HP" "H" "sp3" } { "OH" "O" "sp3" } { "OS" "O" "sp3" } { "O" "O" "sp2" } { "O2" "O" "sp2" } { "OW" "O" "sp3" } { "CT" "C" "sp3" } { "CH" "C" "sp3" } { "C2" "C" "sp3" } { "C3" "C" "sp3" } { "C" "C" "sp2" } { "C*" "C" "sp2" } { "CA" "C" "sp2" } { "CB" "C" "sp2" } { "CC" "C" "sp2" } { "CN" "C" "sp2" } { "CM" "C" "sp2" } { "CK" "C" "sp2" } { "CQ" "C" "sp2" } { "CD" "C" "sp2" } { "CE" "C" "sp2" } { "CF" "C" "sp2" } { "CG" "C" "sp2" } { "CP" "C" "sp2" } { "CI" "C" "sp2" } { "CJ" "C" "sp2" } { "CW" "C" "sp2" } { "CV" "C" "sp2" } { "CR" "C" "sp2" } { "CA" "C" "sp2" } { "CY" "C" "sp2" } { "C0" "C" "sp2" } { "MG" "Mg" "sp3" } { "N" "N" "sp2" } { "NA" "N" "sp2" } { "N2" "N" "sp2" } { "N*" "N" "sp2" } { "NP" "N" "sp2" } { "NQ" "N" "sp2" } { "NB" "N" "sp2" } { "NC" "N" "sp2" } { "NT" "N" "sp3" } { "N3" "N" "sp3" } { "S" "S" "sp3" } { "SH" "S" "sp3" } { "P" "P" "sp3" } { "EP" "" "sp3" } { "F" "F" "sp3" } { "CL" "Cl" "sp3" } { "BR" "Br" "sp3" } { "I" "I" "sp3" } { "FE" "Fe" "sp3" } # things should be there { "IM" "Cl" "sp3" } { "IP" "Na" "sp3" } { "Li" "Li" "sp3" } { "K" "K" "sp3" } { "Rb" "Rb" "sp3" } { "Cs" "Cs" "sp3" } { "Zn" "Zn" "sp3" } { "IB" "Na" "sp3" } # "new" types { "H0" "H" "sp3" } } # # Load the main parameter set. # parm99 =3D loadamberparams parm99.dat parmpol=3D loadamberparams frcmod.ff02pol.r1 # # Load DNA/RNA libraries # loadOff all_nucleic02.lib # # Load main chain and terminating=20 # amino acid libraries. # loadOff all_amino02.r1.lib loadOff all_aminoct02.lib loadOff all_aminont02.lib loadOff ions94.lib loadOff solvents.lib HOH =3D PL3 WAT =3D PL3 #HOH =3D TP3 #WAT =3D TP3 # # Define the PDB name map for the amino acids and DNA. # addPdbResMap { { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } { 0 "HID" "NHID" } { 1 "HID" "CHID" } { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } { 0 "MET" "NMET" } { 1 "MET" "CMET" } { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } { 0 "SER" "NSER" } { 1 "SER" "CSER" } { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } { 0 "C5" "DC5" } { 0 "G5" "DG5" } { 0 "A5" "DA5" } { 0 "T5" "DT5" } { 1 "C3" "DC3" } { 1 "G3" "DG3" } { 1 "A3" "DA3" } { 1 "T3" "DT3" } } addPdbAtomMap { { "O5*" "O5'" } { "C5*" "C5'" } { "C4*" "C4'" } { "O4*" "O4'" } { "C3*" "C3'" } { "O3*" "O3'" } { "C2*" "C2'" } { "C1*" "C1'" } { "C5M" "C7" } { "H1*" "H1'" } { "H2*1" "H2'1" } { "H2*2" "H2'2" } { "H3*" "H3'" } { "H4*" "H4'" } { "H5*1" "H5'1" } { "H5*2" "H5'2" } # old ff atom names -> new { "O1'" "O4'" } { "OA" "O1P" } { "OB" "O2P" } } # # assumed that most often proteins use HIE # NHIS =3D NHIE HIS =3D HIE CHIS =3D CHIE loadamberprep urea.prep loadamberparams Parm4Urea.dat loadamberparams frcmod.pol3 test=3Dloadpdb "Urea90cVb_md38.pdb" charge test #addions test Na+ 0 solvateBox test TIP3PBOX {8.4 8.4 30.0} set test box { 16.1442996 16.6257456 100.0000000 } saveamberparmpol test Urea90cVpol.prmtop Urea90cVpol.inpcrd savepdb test Urea90cVpol.pdb quit oooooooooooooooooooooooooooooooooooooooo Any advice? Thanks a lot, Yubo =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=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 Yubo Fan Ph.D Email: yubofan() mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =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=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 ------=_NextPart_000_0007_01C7F9F4.C6D2F900 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, everyone,
 
I am working on a urea-water system by = using Amber=20 9. The MD simulations have been working fine for both TIP3P and TIP4P = models.=20 But, when I applied polarizable force field for the urea-TIP3P system, = the Epolz=20 term (in the output file) goes weird. The values increase from -10100 to = 7900=20 for each 1-ns trajectory. The input file and leaprc files are shown=20 below:
 
INPUT:
oooooooooooooooooooooooooooooooooooooooo
urea in water (7.626 M): 1 ns=20 MD
 &cntrl
  imin =3D 0, irest =3D 1, ntx =3D = 5,
  ntb =3D=20 1, ntp =3D 0,
  cut =3D 10, ntr =3D 0,
  ntc =3D 2, ntf = =3D 2,
 =20 tempi =3D 300.0, temp0 =3D 300.0,
  ntt =3D 3, gamma_ln =3D = 1.0,
 =20 nstlim =3D 500000, dt =3D 0.002,
  ntpr =3D 250, ntwx =3D 250, = ntwr =3D=20 10000,
  nscm =3D 100, ioutfm =3D 1, iwrap=3D1,
  vlimit = =3D 20.0, ipol=20 =3D = 1,
 /
oooooooooooooooooooooooooooooooooooooooo
 
LEAPRC:
oooooooooooooooooooooooooooooooooooooooo
logFile leap.log
#
# ----- leaprc = for loading=20 the 2002 pol. force field, no lone=20 pairs
#       assumes that any = unspecified=20 nucleic acids are DNA
#
# ----- leaprc for loading the modified = mainchain=20 torsion parameters
#       as described = in
#       Wang et al, (2006) JCC, = 27(6),=20 781-790
#
# load atom type = hybridizations
#
addAtomTypes=20 {
 { "H"   "H" "sp3" }
 { "HO"  "H" "sp3" = }
 { "HS"  "H" "sp3" }
 { "H1"  "H" "sp3" = }
 {=20 "H2"  "H" "sp3" }
 { "H3"  "H" "sp3" }
 { = "H4" =20 "H" "sp3" }
 { "H5"  "H" "sp3" }
 { "HW"  "H" = "sp3"=20 }
 { "HC"  "H" "sp3" }
 { "HA"  "H" "sp3" = }
 {=20 "HP"  "H" "sp3" }
 { "OH"  "O" "sp3" }
 { = "OS" =20 "O" "sp3" }
 { "O"   "O" "sp2" }
 { "O2"  = "O"=20 "sp2" }
 { "OW"  "O" "sp3" }
 { "CT"  "C" = "sp3"=20 }
 { "CH"  "C" "sp3" }
 { "C2"  "C" "sp3" = }
 {=20 "C3"  "C" "sp3" }
 { "C"   "C" "sp2" }
 { = "C*"  "C" "sp2" }
 { "CA"  "C" "sp2" }
 { = "CB" =20 "C" "sp2" }
 { "CC"  "C" "sp2" }
 { "CN"  "C" = "sp2"=20 }
 { "CM"  "C" "sp2" }
 { "CK"  "C" "sp2" = }
 {=20 "CQ"  "C" "sp2" }
 { "CD"  "C" "sp2" }
 { = "CE" =20 "C" "sp2" }
 { "CF"  "C" "sp2" }
 { "CG"  "C" = "sp2"=20 }
 { "CP"  "C" "sp2" }
 { "CI"  "C" "sp2" = }
 {=20 "CJ"  "C" "sp2" }
 { "CW"  "C" "sp2" }
 { = "CV" =20 "C" "sp2" }
 { "CR"  "C" "sp2" }
 { "CA"  "C" = "sp2"=20 }
 { "CY"  "C" "sp2" }
 { "C0"  "C" "sp2" = }
 {=20 "MG"  "Mg" "sp3" }
 { "N"   "N" "sp2" = }
 {=20 "NA"  "N" "sp2" }
 { "N2"  "N" "sp2" }
 { = "N*" =20 "N" "sp2" }
 { "NP"  "N" "sp2" }
 { "NQ"  "N" = "sp2"=20 }
 { "NB"  "N" "sp2" }
 { "NC"  "N" "sp2" = }
 {=20 "NT"  "N" "sp3" }
 { "N3"  "N" "sp3" }
 {=20 "S"   "S" "sp3" }
 { "SH"  "S" "sp3" }
 { = "P"   "P" "sp3" }
 { "EP"  ""  "sp3" = }
 {=20 "F"   "F" "sp3" }
 { "CL"  "Cl" "sp3" = }
 {=20 "BR"  "Br" "sp3" }
 { "I"   "I"  "sp3" = }
 {=20 "FE"  "Fe" "sp3" }
# things should be=20 there
        { "IM"  "Cl" = "sp3"=20 }
        { "IP"  "Na" "sp3"=20 }
        { "Li"  "Li"  = "sp3"=20 }
        { "K"  "K"  = "sp3"=20 }
        { "Rb"  "Rb"  = "sp3"=20 }
        { "Cs"  "Cs"  = "sp3"=20 }
        { "Zn"  "Zn"  = "sp3"=20 }
        { "IB"  "Na"  = "sp3"=20 }
# "new" types
        { = "H0" =20 "H" "sp3" }
 
}
#
# Load the main = parameter=20 set.
#
parm99 =3D loadamberparams parm99.dat
parmpol=3D = loadamberparams=20 frcmod.ff02pol.r1
#
# Load DNA/RNA libraries
#
loadOff=20 all_nucleic02.lib
#
# Load main chain and terminating=20
# amino acid libraries.
#
loadOff = all_amino02.r1.lib
loadOff=20 all_aminoct02.lib
loadOff all_aminont02.lib
 
loadOff ions94.lib
loadOff = solvents.lib
HOH =3D=20 PL3
WAT =3D PL3
#HOH =3D TP3
#WAT =3D TP3
 
#
# Define the PDB name map for = the amino=20 acids and DNA.
#
addPdbResMap {
  { 0 "ALA" "NALA" } { 1 = "ALA"=20 "CALA" }
  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
  { 0 = "ASN"=20 "NASN" } { 1 "ASN" "CASN" }
  { 0 "ASP" "NASP" } { 1 "ASP" = "CASP"=20 }
  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
  { 0 "CYX" = "NCYX" } {=20 1 "CYX" "CCYX" }
  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" = }
  { 0=20 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
  { 0 "GLY" "NGLY" } { 1 "GLY" = "CGLY"=20 }
  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
  { 0 "HIE" = "NHIE" } {=20 1 "HIE" "CHIE" }
  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" = }
  { 0=20 "ILE" "NILE" } { 1 "ILE" "CILE" }
  { 0 "LEU" "NLEU" } { 1 "LEU" = "CLEU"=20 }
  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
  { 0 "MET" = "NMET" } {=20 1 "MET" "CMET" }
  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" = }
  { 0=20 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
  { 0 "SER" "NSER" } { 1 "SER" = "CSER"=20 }
  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
  { 0 "TRP" = "NTRP" } {=20 1 "TRP" "CTRP" }
  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" = }
  { 0=20 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
  { 0 "HIS" "NHIS" } { 1 "HIS" = "CHIS"=20 }
  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" = }
  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" = }
  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" = }
  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" = }
  { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { = "GN"=20 "DGN" }
  { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" = } {=20 "AN" "DAN" }
  { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" = "DC" }=20 { "CN" "DCN" }
  { 0 "T" "DT5"  } { 1 "T" "DT3"  } { = "T" "DT"=20 } { "TN" "DTN" }
  { 0 "C5" "DC5" }
  { 0 "G5" "DG5" = }
 =20 { 0 "A5" "DA5" }
  { 0 "T5" "DT5" }
  { 1 "C3" "DC3" = }
 =20 { 1 "G3" "DG3" }
  { 1 "A3" "DA3" }
  { 1 "T3" "DT3"=20 }
 
}
 
addPdbAtomMap {
  { "O5*" "O5'" = }
 =20 { "C5*" "C5'" }
  { "C4*" "C4'" }
  { "O4*" "O4'" = }
  {=20 "C3*" "C3'" }
  { "O3*" "O3'" }
  { "C2*" "C2'" = }
  {=20 "C1*" "C1'" }
  { "C5M" "C7"  }
  { "H1*" "H1'" = }
 =20 { "H2*1" "H2'1" }
  { "H2*2" "H2'2" }
  { "H3*" "H3'"=20 }
  { "H4*" "H4'" }
  { "H5*1" "H5'1" }
  { = "H5*2"=20 "H5'2" }
# old ff atom names -> new
  { "O1'" "O4'" = }
  {=20 "OA"  "O1P" }
  { "OB"  "O2P" }
}
 
#
# assumed that most often proteins = use=20 HIE
#
NHIS =3D NHIE
HIS =3D HIE
CHIS =3D = CHIE
loadamberprep=20 urea.prep
loadamberparams Parm4Urea.dat
loadamberparams=20 frcmod.pol3
test=3Dloadpdb "Urea90cVb_md38.pdb"
charge = test
#addions test=20 Na+ 0
solvateBox test TIP3PBOX {8.4 8.4 30.0}
set test box {=20 16.1442996  16.6257456 100.0000000 }
saveamberparmpol test=20 Urea90cVpol.prmtop Urea90cVpol.inpcrd
savepdb test=20 Urea90cVpol.pdb
quit
oooooooooooooooooooooooooooooooooooooooo
 
Any advice?
 
Thanks a lot,
 
Yubo
=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=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
Yubo=20 Fan =20 Ph.D           &nb= sp;=20 Email: yubofan() mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=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=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
------=_NextPart_000_0007_01C7F9F4.C6D2F900-- From owner-chemistry@ccl.net Tue Sep 18 15:58:00 2007 From: "John McKelvey jmmckel..gmail.com" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35197-070918132459-8530-+e1Q5mSn6t/oBLctG/BMpQ : server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_22343_20992245.1190129480664" Date: Tue, 18 Sep 2007 11:31:20 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel-*-gmail.com] ------=_Part_22343_20992245.1190129480664 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline One has to be careful using mndo/d with main group elements. Where hypervalent elements are not involved it should probably give about the sam= e results as mndo. How does plain mndo work for you under these circumstances? I would put my bets on using MOPAC-2007; also try PM6 therein. My $0.02. john McKelvey On 9/18/07, Sina T=FCreli sinatureli+/-gmail.com wrote: > > Hmm for some reasons my questions did not appear... So I will post them > here > > When I do geometry optimization with mndo/d on a biomolecule after some > time some of the atoms bond to each other while doing the same optimizati= on > in spartan with am1 or pm3 does not yield such results. What may be the > cause of this, and how can I prevent that? > > And also when I try to run mopac from hyperchem, it opens the input file > but then it gives a "program teriminated with exit code 0" > error.. What may be the cause of this? > > Thanks.. > > > On 9/18/07, Sina T reli sinaturelia/gmail.com > wrote: > > > > > > Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com] > > Hello, > > > > I have a few questions regarding hyperchem. > > > > > > > > > > E-mail to subscribers: CHEMISTRY+/-ccl.net or use:> > > > E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or use> > > > > > Before posting, check wait time at: > > http://www.ccl.net> > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > > > > > ------=_Part_22343_20992245.1190129480664 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline One has to be careful using mndo/d with main group elements.  Where hy= pervalent elements are not involved it should probably give about the same = results as mndo.  How does plain mndo work for you under these circums= tances?  I would put my bets on using MOPAC-2007; also try PM6 therein= .

My $0.02.

john McKelvey

On 9/18/07, Sina T=FCreli sinatureli+/-gmail.com < owner-chemistry(a)ccl.net> wrote:
Hmm for some reasons my questions did not appea= r... So I will post them here

When I do geometry optimization with mndo/d on a biomolecule after = some time some of the atoms bond to each other while doing the same optimiz= ation in spartan with am1 or pm3 does not yield such results. What may be t= he cause of this, and how can I prevent that?

And also when I try to run mopac from hyperchem, it opens the input= file but then it gives a "program teriminated with exit code 0"<= br>error.. What may be the cause of this?

Thanks..


On 9/18/07, Sina = T reli sinaturelia/gmail.com < owner-chemistry+/-ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinature= li]![gmail.com]
Hello,

I have a = few questions regarding hyperchem.




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------=_Part_22343_20992245.1190129480664-- From owner-chemistry@ccl.net Tue Sep 18 16:28:00 2007 From: "anamika awasthi anamikaawasthi28*_*rediffmail.com" To: CCL Subject: CCL: query reg. docking followed by Dynamics Message-Id: <-35198-070917060551-4550-oed03qRzXpEKAJbloTv9fg_-_server.ccl.net> X-Original-From: "anamika awasthi" Content-type: multipart/alternative; boundary="Next_1190019800---0-202.54.124.239-16829" Date: 17 Sep 2007 09:03:20 -0000 MIME-Version: 1.0 Sent to CCL by: "anamika awasthi" [anamikaawasthi28|a|rediffmail.com] This is a multipart mime message --Next_1190019800---0-202.54.124.239-16829 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =0AHello Friend,=0A =0A1. no we cant see as you are saying , that can be = show by only animation =0A2. you can find lots of paper, sciencedirect.com = is precious website for this.=0A3. Molecular dynamics and simulation does n= ot exist, Molecular Dynamics Simulation is one term. MD simulation is relai= ble in terms of computational work, this needs proper simulation and valida= tion.=0A=0A with regards =0A Anamika=0A=0A=0AOn Sun, 16 Sep 2007 Kalyan ch= aitanya kalyanpulipaka%x%gmail.com wrote :=0A>Hi all,=0A>=0A>I have a doubt= , I am now working on Docking and i learnt that M.Dynamics and=0A>simulatio= ns would be very useful and efficient way of understanding how=0A>exactly t= wo molecules are interacting with each other, i have GROMACS,=0A>TINKER and= NAMD for the same purpose, but can you tell me-=0A>=0A>1. Is it that we ca= n see ligand and receptor coming together and trying to=0A>fit with differe= nt conformations and finally binding itself with a stable=0A>conformation.= =0A>=0A>2.can any one refer any publication papers who have done Docking fo= llowed by=0A>Dynamics and simulations in showing the interactions.=0A>=0A>3= . how relaiable is M.Dynamics and simulations.=0A>=0A>Thanks in advance,=0A= >=0A>Regards,=0A>=0A>P.Kalyan=0A --Next_1190019800---0-202.54.124.239-16829 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A 
=0AHello Friend,
=0A
=0A1. no we cant see as you ar= e saying , that can be show by only animation
=0A2. you can find lots o= f paper, sciencedirect.com is precious website for this.
=0A3. Molecular= dynamics and simulation does not exist, Molecular Dynamics Simulation is o= ne term. MD simulation is relaible in terms of computational work, this nee= ds proper simulation and validation.
=0A
=0A with regards
=0A&nbs= p; Anamika
=0A
=0A
=0AOn Sun, 16 Sep 2007 Kalyan chaitanya kalyanp= ulipaka%x%gmail.com wrote :
=0A>Hi all,
=0A>
=0A>I have a= doubt, I am now working on Docking and i learnt that M.Dynamics and
=0A= >simulations would be very useful and efficient way of understanding how=
=0A>exactly two molecules are interacting with each other, i have GR= OMACS,
=0A>TINKER and NAMD for the same purpose, but can you tell me-=
=0A>
=0A>1. Is it that we can see ligand and receptor coming t= ogether and trying to
=0A>fit with different conformations and finall= y binding itself with a stable
=0A>conformation.
=0A>
=0A>= ;2.can any one refer any publication papers who have done Docking followed = by
=0A>Dynamics and simulations in showing the interactions.
=0A&g= t;
=0A>3. how relaiable is M.Dynamics and simulations.
=0A>
= =0A>Thanks in advance,
=0A>
=0A>Regards,
=0A>
=0A&g= t;P.Kalyan
=0A=0A

=0A

=0A
3D'garnier
--Next_1190019800---0-202.54.124.239-16829-- From owner-chemistry@ccl.net Tue Sep 18 17:06:01 2007 From: "Lothar Terfloth lothar.terfloth]*[mol-net.com" To: CCL Subject: CCL: Smiles -> 2D & 3D Message-Id: <-35199-070918090910-9251-4l/hrEC/IHZDvjZ1pYtjvw~!~server.ccl.net> X-Original-From: Lothar Terfloth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Sep 2007 14:14:21 +0200 MIME-Version: 1.0 Sent to CCL by: Lothar Terfloth [lothar.terfloth|-|mol-net.com] Dear all, concerning the conversion of SMILES into 2D and 3D coordinates I would like to direct your attention to Molecular Networks solutions for these tasks: 2DCOOR and CORINA You can find more information about 2D and 3D coordinate generation below the following URLs: http://www.mol-net.com/software/category/gen2dcoord.html http://www.mol-net.com/software/category/gen3dcoord.html Online demos are available at the URLs: http://www.mol-net.com/online_demos/2dcoor_demo.html and http://www.mol-net.com/online_demos/corina_demo.html Evaluation versions are available from our download area: http://www.mol-net.com/php/profile.php With kind regards, Lothar Terfloth -------------------------------------------------------- Dr. Lothar Terfloth Tel. +49-9131-9790623 Molecular Networks GmbH Fax: +49-9131-815 669 Henkestr. 91 D-91052 Erlangen Germany email: Lothar.Terfloth : mol-net.com www: http://www.mol-net.com -------------------------------------------------------- Ivanciuc, Ovidiu I. oiivanci _ utmb.edu wrote: > Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci++utmb.edu] > > > for SMILES -> 2D: GIF/PNG-Creator > http://cactus.nci.nih.gov/services/gifcreator/ > > for SMILES -> 2D &3D: SDF, PDB, MOL > http://cactus.nci.nih.gov/services/translate/ > > O. > -- -------------------------------------------------------- Dr. Lothar Terfloth Tel. +49-9131-9790623 Molecular Networks GmbH Fax: +49-9131-815 669 Henkestr. 91 D-91052 Erlangen Germany email: Lothar.Terfloth : mol-net.com www: http://www.mol-net.com -------------------------------------------------------- From owner-chemistry@ccl.net Tue Sep 18 17:39:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli++gmail.com" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35200-070918163613-3305-7XQA3kyJJ6E/9caoklREpQ**server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_6626_9944787.1190147740652" Date: Tue, 18 Sep 2007 23:35:40 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli++gmail.com] ------=_Part_6626_9944787.1190147740652 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have a mg atom in my molecule that is ligated so I can not use mndo only... I also have the need to freeze many atoms thus it would be a pain t= o use mopac from conseole cause I have to manually change lots of 1's to 0's. Is there any gui you know of that can do that? I tried VEGA but VEGA does not support PM6. And I have problems running mopac from hyperchem... On 9/18/07, John McKelvey jmmckel..gmail.com wrote: > > One has to be careful using mndo/d with main group elements. Where > hypervalent elements are not involved it should probably give about the s= ame > results as mndo. How does plain mndo work for you under these > circumstances? I would put my bets on using MOPAC-2007; also try PM6 > therein. > > My $0.02. > > john McKelvey > > On 9/18/07, Sina T=FCreli sinatureli+/-gmail.com < owner-chemistry^^ccl.n= et> > wrote: > > > > Hmm for some reasons my questions did not appear... So I will post them > > here > > > > When I do geometry optimization with mndo/d on a biomolecule after some > > time some of the atoms bond to each other while doing the same optimiza= tion > > in spartan with am1 or pm3 does not yield such results. What may be the > > cause of this, and how can I prevent that? > > > > And also when I try to run mopac from hyperchem, it opens the input fil= e > > but then it gives a "program teriminated with exit code 0" > > error.. What may be the cause of this? > > > > Thanks.. > > > > > > On 9/18/07, Sina T reli sinaturelia/gmail.com > > wrote: > > > > > > > > > Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com] > > > Hello, > > > > > > I have a few questions regarding hyperchem. > > > > > > > > > > > > > > > E-mail to subscribers: CHEMISTRY+/-ccl.net or use: > > > > > > > > > E-mail to administrators: > > > CHEMISTRY-REQUEST+/-= ccl.netor use> > > > > > > > > Before posting, check wait time at: > > > http://www.ccl.net> > > Conferences: > > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > > search)> > > > > > > > > > > > > > > > > > ------=_Part_6626_9944787.1190147740652 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have a mg atom in my molecule that is ligated so I can not use mndo only.= .. I also have the need to freeze many atoms thus it would be a pain to use= mopac from conseole cause I have to manually change lots of 1's to 0&#= 39;s. Is there any gui you know of that can do that? I tried VEGA but VEGA = does not support PM6. And I have problems running mopac from hyperchem...

On 9/18/07, John McKelvey jmmckel..gmail.com <owner-chemistry!^!ccl.net> wrote:
One has to be careful using mndo/d with main group elements.  Where hy= pervalent elements are not involved it should probably give about the same = results as mndo.  How does plain mndo work for you under these circums= tances?  I would put my bets on using MOPAC-2007; also try PM6 therein= .

My $0.02.

john McKelvey

On 9/18/07, Sina T=FCre= li sinatureli+/- gmail.com < owner-chemistry^^ccl.net> wrote:
Hmm for some reasons = my questions did not appear... So I will post them here

When I do geometry optimization with mndo/d on a biomolecule after = some time some of the atoms bond to each other while doing the same optimiz= ation in spartan with am1 or pm3 does not yield such results. What may be t= he cause of this, and how can I prevent that?

And also when I try to run mopac from hyperchem, it opens the input= file but then it gives a "program teriminated with exit code 0"<= br>error.. What may be the cause of this?

Thanks..


On 9/18/07, Sina = T reli sinaturelia/gmail.com < owner-chemistry+/-ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinature= li]![gmail.com]
Hello= ,

I have a few questions regarding hyperchem.




E-mail to subscribers:=20 CHEMISTRY+/-ccl.net or use:
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------=_Part_6626_9944787.1190147740652-- From owner-chemistry@ccl.net Tue Sep 18 18:13:01 2007 From: "Ivanciuc, Ovidiu I. oiivanci++utmb.edu" To: CCL Subject: CCL: query reg. docking followed by Dynamics Message-Id: <-35201-070918170741-25976-eJX8e3k/uaMacvxBZLCB/g~!~server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 18 Sep 2007 16:05:30 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci^^utmb.edu] >2.can any one refer any publication papers who have done Docking = followed by >Dynamics and simulations in showing the interactions. Go to PubMed, http://www.ncbi.nlm.nih.gov/sites/entrez and search with the keywords: docking "molecular dynamics" O. From owner-chemistry@ccl.net Tue Sep 18 19:49:00 2007 From: "John McKelvey jmmckel##gmail.com" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35202-070918194409-19222-6EzMuIDat9IbTSE1t7eSYg{}server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_24639_24375633.1190159021592" Date: Tue, 18 Sep 2007 19:43:41 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel()gmail.com] ------=_Part_24639_24375633.1190159021592 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline MOPAC2007 is free...and extremely fast. Try PM6 in it. It has a gui that works with WindowsXP. Google MrMOPAC to locate Jimmy Stewart. Cheers! John McKelvey On 9/18/07, Sina T=FCreli sinatureli++gmail.com wrote: > > I have a mg atom in my molecule that is ligated so I can not use mndo > only... I also have the need to freeze many atoms thus it would be a pain= to > use mopac from conseole cause I have to manually change lots of 1's to 0'= s. > Is there any gui you know of that can do that? I tried VEGA but VEGA does > not support PM6. And I have problems running mopac from hyperchem... > > On 9/18/07, John McKelvey jmmckel..gmail.com > wrote: > > > > One has to be careful using mndo/d with main group elements. Where > > hypervalent elements are not involved it should probably give about the= same > > results as mndo. How does plain mndo work for you under these > > circumstances? I would put my bets on using MOPAC-2007; also try PM6 > > therein. > > > > My $0.02. > > > > john McKelvey > > > > On 9/18/07, Sina T=FCreli sinatureli+/- gmail.com > > > wrote: > > > > > > Hmm for some reasons my questions did not appear... So I will post > > > them here > > > > > > When I do geometry optimization with mndo/d on a biomolecule after > > > some time some of the atoms bond to each other while doing the same > > > optimization in spartan with am1 or pm3 does not yield such results. = What > > > may be the cause of this, and how can I prevent that? > > > > > > And also when I try to run mopac from hyperchem, it opens the input > > > file but then it gives a "program teriminated with exit code 0" > > > error.. What may be the cause of this? > > > > > > Thanks.. > > > > > > > > > On 9/18/07, Sina T reli sinaturelia/gmail.com > > > wrote: > > > > > > > > > > > > Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com] > > > > Hello, > > > > > > > > I have a few questions regarding hyperchem. > > > > > > > > > > > > > > > > > > > > E-mail to subscribers: CHEMISTRY+/-ccl.net or use: > > > > > > > > > > > > E-mail to administrators: > > > > CHEMISTRY-REQUEST+= /-ccl.netor use> > > > > > > > > > > > Before posting, check wait time at: > > > > http://www.ccl.net> > > > Conferences: > > > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > > > search)> > > > > > > > > > > > > > > > > > > > > > > > > > ------=_Part_24639_24375633.1190159021592 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline MOPAC2007 is free...and extremely fast.   Try PM6 in it.  It has = a gui that works with WindowsXP.   Google MrMOPAC to locate Jimmy= Stewart.



Cheers!

John McKelvey

On 9/18/07, Sina T=FCreli sinatureli++gmail.c= om <owner-chemistry**ccl.n= et> wrote:
I have a mg atom in my molecule that is ligated so I can not use mndo only.= .. I also have the need to freeze many atoms thus it would be a pain to use= mopac from conseole cause I have to manually change lots of 1's to 0&#= 39;s. Is there any gui you know of that can do that? I tried VEGA but VEGA = does not support PM6. And I have problems running mopac from hyperchem...

On 9/18/07, John McKelvey jmmckel..gmail.com < owner-chemistry-#-ccl.net> wrote:
One has to be careful using mndo/d with main group elements.  Where hy= pervalent elements are not involved it should probably give about the same = results as mndo.  How does plain mndo work for you under these circums= tances?  I would put my bets on using MOPAC-2007; also try PM6 therein= .

My $0.02.

john McKelvey

On 9/18/07, Sina T=FCreli sinaturel= i+/- gmail.com < owner-chemistry^^ccl.net> wrote:
Hmm for some reasons my questions= did not appear... So I will post them here

When I do geometry optimization with mndo/d on a biomolecule after = some time some of the atoms bond to each other while doing the same optimiz= ation in spartan with am1 or pm3 does not yield such results. What may be t= he cause of this, and how can I prevent that?

And also when I try to run mopac from hyperchem, it opens the input= file but then it gives a "program teriminated with exit code 0"<= br>error.. What may be the cause of this?

Thanks..


On 9/18/07, Sina = T reli sinaturelia/gmail.com < owner-chemistry+/-ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinature= li]![gmail.com]
Hello,

I h= ave a few questions regarding hyperchem.




E-mail to subscribers:=20 CHEMISTRY+/-ccl.net or use:
&= nbsp;     

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Job: http://server.ccl.net/chemistry/announcements/conferences/
=
Search Messages: http://www.ccl.net/ht= dig   (login: ccl, Password: search)

 &n= bsp;    htt= p://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/




=




------=_Part_24639_24375633.1190159021592-- From owner-chemistry@ccl.net Tue Sep 18 20:31:01 2007 From: "Andrey.Bliznyuk*anu.edu.au" To: CCL Subject: CCL: query reg. docking followed by Dynamics Message-Id: <-35203-070918200626-26544-+lF2LP0yYsqgWnez8hTc8Q{=}server.ccl.net> X-Original-From: Andrey.Bliznyuk:-:anu.edu.au Date: Wed, 19 Sep 2007 09:33:49 +1000 Sent to CCL by: Andrey.Bliznyuk]*[anu.edu.au > >2.can any one refer any publication papers who have done Docking followed by > >Dynamics and simulations in showing the interactions. > > Go to PubMed, http://www.ncbi.nlm.nih.gov/sites/entrez > and search with the keywords: docking "molecular dynamics" or look at the following review: Alonso H. Bliznyuk AA. Gready JE. "Combining docking and molecular dynamic simulations in drug design" [Review]. Medicinal Research Reviews. 26(5):531-568, 2006 Sep. Andrey From owner-chemistry@ccl.net Tue Sep 18 21:13:00 2007 From: "David Gallagher gallagher.da_+_gmail.com" To: CCL Subject: CCL: Hyperchem and Mopac2007 Message-Id: <-35204-070918204135-14247-lEEf4VG45CD/Bb+ZIspXYQ],[server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_5549281==.ALT" Date: Tue, 18 Sep 2007 17:35:06 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da###gmail.com] --=====================_5549281==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable A list of free GUIs for MOPAC2007 is shown at=20 http://www.openmopac.net/resellers.html Cheers, David Gallagher CAChe Research At 04:43 PM 9/18/2007, John McKelvey jmmckel##gmail.com wrote: >MOPAC2007 is free...and extremely fast. Try=20 >PM6 in it. It has a gui that works with=20 >WindowsXP. Google MrMOPAC to locate Jimmy Stewart. > > > >Cheers! > >John McKelvey > >On 9/18/07, Sina T=FCreli sinatureli++gmail.com=20 ><owner-chemistry-,-ccl.net> wrote: >I have a mg atom in my molecule that is ligated=20 >so I can not use mndo only... I also have the=20 >need to freeze many atoms thus it would be a=20 >pain to use mopac from conseole cause I have to=20 >manually change lots of 1's to 0's. Is there any=20 >gui you know of that can do that? I tried VEGA=20 >but VEGA does not support PM6. And I have=20 >problems running mopac from hyperchem... > >On 9/18/07, John McKelvey jmmckel..gmail.com=20 >< owner-chemistry-#-ccl.net> wrote: >One has to be careful using mndo/d with main=20 >group elements. Where hypervalent elements are=20 >not involved it should probably give about the=20 >same results as mndo. How does plain mndo work=20 >for you under these circumstances? I would put=20 >my bets on using MOPAC-2007; also try PM6 therein. > >My $0.02. > >john McKelvey > >On 9/18/07, Sina T=FCreli=20 >sinatureli+/- gmail.com=20 >< owner-chemistry^^ccl.net> wrote: >Hmm for some reasons my questions did not appear... So I will post them= here > >When I do geometry optimization with mndo/d on a=20 >biomolecule after some time some of the atoms=20 >bond to each other while doing the same=20 >optimization in spartan with am1 or pm3 does not=20 >yield such results. What may be the cause of this, and how can I prevent= that? > >And also when I try to run mopac from hyperchem,=20 >it opens the input file but then it gives a=20 >"program teriminated with exit code 0" >error.. What may be the cause of this? > >Thanks.. > > >On 9/18/07, Sina T reli sinaturelia/gmail.com=20 >< owner-chemistry+/-ccl.net> wrote: > >Sent to CCL by: "Sina T reli" [sinatureli]![gmail.com] >Hello, > >I have a few questions regarding hyperchem. > > > > >E-mail to subscribers: CHEMISTRY+/-ccl.net or= use: > > >E-mail to administrators:=20 >CHEMISTRY-REQUEST+/-ccl.net or use >=20 >http://www.ccl.net/cgi-bin= /ccl/send_ccl_message=20> > >Before posting, check wait time at: http://www.ccl.net > >Job: http://www.ccl.net/jobs >Conferences:=20 >http://server.c= cl.net/chemistry/announcements/conferences/ > >Search Messages:=20 >http://www.ccl.net/htdig=20 >(login: ccl, Password: search) > > http://www.ccl.net/spammers.txt > >RTFI:=20 >http://www.ccl.net/che= mistry/aboutccl/instructions/ > > > > > > > --=====================_5549281==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable A list of free GUIs for MOPAC2007 is shown at http://www.openmopac.net/resellers.html

Cheers,
David Gallagher
CAChe Research


At 04:43 PM 9/18/2007, John McKelvey jmmckel##gmail.com wrote:
MOPAC2007 is free...and extremely fast.   Try PM6 in it.  It has a gui that works with WindowsXP.   Google MrMOPAC to locate Jimmy Stewart.



Cheers!

John McKelvey

On 9/18/07, Sina T=FCreli sinatureli++gmail.com < owner-chemistry-,-ccl.net> wrote:
I have a mg atom in my molecule that is ligated so I can not use mndo only... I also have the need to freeze many atoms thus it would be a pain to use mopac from conseole cause I have to manually change lots of 1's to 0's. Is there any gui you know of that can do that? I tried VEGA but VEGA does not support PM6. And I have problems running mopac from hyperchem...

On 9/18/07, John McKelvey jmmckel..gmail.com < owner-chemistry-#-ccl.net> wrote:
One has to be careful using mndo/d with main group elements.  Where hypervalent elements are not involved it should probably give about the same results as mndo.  How does plain mndo work for you under these circumstances?  I would put my bets on using MOPAC-2007; also try PM6 therein.

My $0.02.

john McKelvey

On 9/18/07, Sina T=FCreli sinatureli+/- gmail.com < owner-chemistry^^ccl.net> wrote:
Hmm for some reasons my questions did not appear... So I will post them here

When I do geometry optimization with mndo/d on a biomolecule after some time some of the atoms bond to each other while doing the same optimization in spartan with am1 or pm3 does not yield such results. What may be the cause of this, and how can I prevent that?

And also when I try to run mopac from hyperchem, it opens the input file but then it gives a "program teriminated with exit code 0"
error.. What may be the cause of this?

Thanks..


On 9/18/07, Sina T reli sinaturelia/gmail.com < owner-chemistry+/-ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinatureli]![gmail.com]
Hello,

I have a few questions regarding hyperchem.




E-mail to subscribers: CHEMISTRY+/-ccl.net or use:
     

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Subscribe/Unsubscribe:
     

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
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--=====================_5549281==.ALT--