From jkl@ccl.net Mon Apr 21 01:16:45 2003 -0400 Return-Path: Message-Id: Date: Mon, 21 Apr 2003 09:14:17 +0400 From: "Iman Boukhobza" To: Subject: GAMESS: Problem calculating vanadium complexes Dear CCL'S I am currently working on a project that deals with evaluating the formation energy of vanadium complexes. (Comparative study) - I have GAMESS to use - I have atomic coordinates for my complexes - I believe I have converted my atomic coordinates to a z-matrix(Using Winmopac or/and vega) Problems start when I want to use this matrix in GAMESS to find the needed energy. I keep getting the error messages either about the point group, or the coordinates of atoms. I have 3 main concerns: 1- the bond length I got from the conversion are relatively small 2- the symmetry group. Is there any program that helps to find the symmetry group 3- the parameters specified in the input file, ie: the basis set, RHF,...Should I change or replace some of them to run the input file Any help or suggestion would be very much appreciated Thanks in advance Iman Boukhobza Chemistry assistant professor Zayed University Dubai/UAE From chemistry-request@server.ccl.net Mon Apr 21 09:33:50 2003 Received: from cci.cci-29palms.com ([206.135.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3LDXoa25195 for ; Mon, 21 Apr 2003 09:33:50 -0400 Received: from PAVXT983 (mod5.cci-29palms.com [206.135.1.70]) by cci.cci-29palms.com (8.9.3/8.9.3) with SMTP id GAA16064 for ; Mon, 21 Apr 2003 06:34:00 -0700 Message-ID: <003401c3080a$9c45c860$460187ce@PAVXT983> Reply-To: "Gerald J. grott" From: "Gerald J. grott" To: Subject: modeling ion exchange Date: Mon, 21 Apr 2003 06:33:34 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01C307CF.EF152170" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C307CF.EF152170 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable CCL Member: Am so ancient that I watched them assemble the second computer ever = built, with vacuum tubes, etc.,. Now am engaged in reclamation of salts from saline waste waters and = fascinated by what you are doing with computers. I ask if any of you have experience with any program that can be used = for calculating selectivity coefficients to be used in modelling ion = exchange. jerry grott ------=_NextPart_000_0031_01C307CF.EF152170 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

CCL Member:

Am so ancient that I watched = them assemble the=20 second computer ever built, with vacuum tubes, etc.,.

Now am engaged in reclamation of salts = > from saline=20 waste waters and fascinated by what you are doing with = computers.

I ask if any of you have = experience with=20 any program that can be used for calculating selectivity=20 coefficients to be used in modelling ion = exchange.

jerry grott

------=_NextPart_000_0031_01C307CF.EF152170-- From chemistry-request@server.ccl.net Mon Apr 21 07:58:40 2003 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3LBwda23447 for ; Mon, 21 Apr 2003 07:58:39 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Mon, 21 Apr 2003 13:58:10 +0200 Message-ID: <000d01c307fd$a363e8a0$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Daniel Svozil" , References: <20030418113712.GA4321@iveta.uochb.cas.cz> Subject: Re: CCL:Molecular transformation language Date: Mon, 21 Apr 2003 14:00:44 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 It is not a language but a program application, however, several manipulation features of those you'd mentioned can be found in Mol2Mol: http://web.interware.hu/frenzy/mol2mol Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "Daniel Svozil" To: Sent: Friday, April 18, 2003 13:37 Subject: CCL:Molecular transformation language > Hi, > > I am doing some calculations with the molecules differently oriented > each to other and a lot of time takes to prepare the coordinate files > for those system. So I started looking for some possibility how to > automatize this process as much as possible. > > Do you know, is there any programming language or library of the existing > language that offers this functionality? > > Here are some my ideas what should such a system include: > - easy, but powerful way how to select atoms for the transformations > (e.g. select the whole backbone, select all waters in system, select > atoms number 1,3,6, select atoms that are not further than 3 angstroms > from the given atom/point, select all carbons, etc., etc.) > - some sort of clever coordinate systems, so I can say e.g. rotate this > H atom in H2O around the axis defined by thos OH bond, etc. > - the possibility to read/wite at least PDB, XYZ would be also nice > - possibility to calculate different geometric characteristics (bond > lenghts, angles, dihedrals) for the given set of atoms > - simple molecular viewer to check the transformed system (e.g. just > wireframe, with scene rotation/translation/zooming, with the > possibility to measure lengths/angles/dihedrals) > - the language should be interpreted, not compiled > > So far I went through VMD, PyMol, NAB and currently I am ivestigating > MMTK package. VMDs functionality is much broader and I didn't figure > out, how to perform some transformation tasks, though I am sure it can > be done. PyMol has very poor documentation, especially transformation > procedure seem to be undocumented. NAB (http://www.scripps.edu/case/casegr-sh-2.2.html) is a manipulation language for DNA/proteins, but it could probably be used for other systems as well. Unfortunately, I didn't suceed with the compilation under Linux ( > > So to summarize, I didn't find any simple scriptable molecular > transformation system so far. I am sure that such a software would be > interesting for a lot people. Maybe I am looking in the wrong direction. > Any help would be more than appreciated. > > Regards > Dan > > -- > Daniel Svozil, PhD > Institute of Organic Chemistry and Biochemistry > and Center for Complex Molecular Systems and Biomolecules > http://www.molecular.cz/ > Czech Republic > > phone: +420-2-20 183 263 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Apr 21 09:25:58 2003 Received: from srvus010.unitedcatalysts.com ([208.23.162.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3LDPwa25051 for ; Mon, 21 Apr 2003 09:25:58 -0400 Received: by lvlxch02.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Mon, 21 Apr 2003 09:23:47 -0400 Message-ID: <5CF08BBFE6DE97478C1E76E654CAF9089C2674@lvlxch02.unitedcatalysts.com> From: "Shobe, Dave" To: =?iso-8859-1?Q?=27Miquel_Sol=E0=27?= , chemistry@ccl.net Subject: RE: Chemistry and architecture relationships Date: Mon, 21 Apr 2003 09:23:39 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-8c45e5b9-2eb7-47c6-82bf-9ac6f10ad210" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------=_NextPartTM-000-8c45e5b9-2eb7-47c6-82bf-9ac6f10ad210 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C30809.38AE9800" ------_=_NextPart_001_01C30809.38AE9800 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You might want to look at "supramolecular" chemistry, where molecules = are used as "building blocks" to make more complicated structures. = Typically these are held together by hydrogen bonds or similar interactions. =20 There are also articles on molecular versions of the construction toys, "Tinkertoys" and "Meccano", perhaps others. (These are analogies used = by the authors of the papers, but do are not meant to imply any connection = to the companies that manufacture these toys or own the trademarks = thereto). These are typically rigid molecules which react, forming covalently = bonded structures. =20 Hope this helps, --David Shobe S=FCd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. =20 -----Original Message----- From: Miquel Sol=E0 [mailto:miquel.sola@udg.es] Sent: Saturday, April 19, 2003 10:14 AM To: chemistry@ccl.net Subject: CCL:Chemistry and architecture relationships Dear CCLers, I have to give a talk to graduate students in Architecture on tools = used for chemists to display molecular properties. I would like to start the introduction = with a reference to relationships between chemistry and architecture. I know only one clear example of this relation which is the C60 molecule called buckminsterfullerene = for its similarity=20 with the geodesic domes made by the architect Richard Buckminster = Fuller. Do you know=20 other examples? I will post a summary if there is interest. Thanks in advance for your answers. Best regards, Miquel = -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*= - Miquel Sol=E0 =20 Institut de Qu=EDmica Computacional =20 Universitat de Girona =20 Campus Montilivi 17071 Girona, CATALONIA (Spain) =20 Phone +34.972.41.89.12 Cellular-Phone: +34.626.163.580 FAX +34.972.41.83.56 =20 World Wide Web: http://iqc.udg.es/~miquel/mike.html =20 e-mail: miquel.sola@udg.es = -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*= - ------_=_NextPart_001_01C30809.38AE9800 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

You=20 might want to look at "supramolecular" chemistry, where molecules are = used as=20 "building blocks" to make more complicated structures. Typically = these are=20 held together by hydrogen bonds or similar = interactions.

There=20 are also articles on molecular versions of the construction=20 toys, "Tinkertoys" and "Meccano", perhaps others. (These are = analogies used by the authors of the papers, but do are not meant=20 to imply any connection to the companies that manufacture these = toys or own=20 the trademarks thereto). These are typically rigid molecules = which react,=20 forming covalently bonded structures.

Hope=20 this helps,

--David Shobe
S=FCd-Chemie Inc.
phone (502)=20 634-7409
fax (502) 634-7724
email =20 dshobe@sud-chemieinc.com

Don't bother flaming me: I'm behind a=20 firewall.

-----Original Message-----
From: Miquel Sol=E0=20 [mailto:miquel.sola@udg.es]
Sent: Saturday, April 19, 2003 = 10:14=20 AM
To: chemistry@ccl.net
Subject: CCL:Chemistry = and=20 architecture relationships
Dear CCLers,

I have to give a talk = to graduate=20 students in Architecture on tools used for chemists to
display = molecular=20 properties. I would like to start the introduction with a reference=20 to
relationships between chemistry and architecture. I know only = one clear=20 example
of this relation which is the = C60=20 molecule called buckminsterfullerene for its similarity
with the = geodesic=20 domes made by the architect Richard Buckminster Fuller. Do you know =
other=20 examples? I will post a summary if there is interest.=20 Thanks in advance for your answers.

Best = regards,

Miquel
 =
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*=
-
 Miquel Sol=E0                          =20
 Institut de Qu=EDmica Computacional        =20
 Universitat de Girona                  =20
 Campus Montilivi
 17071 Girona, CATALONIA (Spain)         =20
 Phone +34.972.41.89.12
 Cellular-Phone:  +34.626.163.580
 FAX   +34.972.41.83.56                              =20
 World Wide Web: http://iqc.udg.es/~miquel=
/mike.html  =20
 e-mail: miquel.sola@udg.es               =
         =20
 =
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*=
-

------_=_NextPart_001_01C30809.38AE9800-- ------=_NextPartTM-000-8c45e5b9-2eb7-47c6-82bf-9ac6f10ad210-- From chemistry-request@server.ccl.net Mon Apr 21 12:38:49 2003 Received: from antivirus1.its.rochester.edu ([128.151.57.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3LGcna29133 for ; Mon, 21 Apr 2003 12:38:49 -0400 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h3LGcmHs011306 for ; Mon, 21 Apr 2003 12:38:48 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with SMTP id h3LGcm2b011303; Mon, 21 Apr 2003 12:38:48 -0400 (EDT) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.9/8.12.1) with ESMTP id h3LGclHD004162; Mon, 21 Apr 2003 12:38:47 -0400 (EDT) Content-Type: text/plain; charset="iso-8859-1" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: NAMD Support Subject: about the DCD file got from NAMD Date: Mon, 21 Apr 2003 12:38:22 -0400 User-Agent: KMail/1.4.1 References: In-Reply-To: Cc: chemistry@ccl.net MIME-Version: 1.0 Message-Id: <200304211238.22753.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3LGcna29134 Dear Sir: can I use the CHARMM program to analyze the DCD file getting from NAMD? or I have to use XPLOR? wei On Friday 18 April 2003 04:07 pm, you wrote: > Hi, > > Was this the 2.5b1 released binary? I can't say what happened, but it's > probably not your fault. You may want to try a newer 2.5b2 test binary > from http://www.ks.uiuc.edu/~jim/tmp/NAMD_build_2003-Apr-04.23261/ > > -Jim > > On Mon, 14 Apr 2003, wei wrote: > > Dear Sir: > > > > Sorry for bother you again. We I try to run NAMD on 6 processors, the > > simulation broke down after random steps ( from 400 to 8600), and gave > > out the error message like following, my command line is " charmrun > > ++debugger gdb +p8 namd2 > log ". and the configuration file is attached > > at the end of this mail.I will really appreciate you comment and help. > > > > ------------- Processor 2 Exiting: Caught Signal ------------ > > Signal: segmentation violation > > Suggestion: Try running with '++debug', or linking with '-memory > > paranoid'. Stack Traceback: > > [0] /lib/libc.so.6 [0x401836e8] > > [1] /usr/local/bin/namd2 [0x81da09c] > > [2] malloc+0x17 [0x81dada7] > > [3] malloc_nomigrate+0x12 [0x81daf5e] > > [4] CmiAlloc+0x15 [0x81cb385] > > [5] AssembleDatagram+0x51 [0x81c74e9] > > [6] AssembleReceivedDatagrams+0x58 [0x81c7710] > > [7] IntegrateMessageDatagram+0xd8 [0x81c7818] > > [8] ReceiveDatagram+0x1d8 [0x81c7ccc] > > [9] /usr/local/bin/namd2 [0x81c7da8] > > [10] /usr/local/bin/namd2 [0x81c4e1c] > > [11] /lib/libc.so.6 [0x401836e8] > > [12] _ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP7Results+0x3fb > > [0x80d96bb] [13] _ZN16ComputePatchPair6doWorkEv+0x81 [0x80e6d01] > > [14] > > _ZN19CkIndex_WorkDistrib31_call_enqueueWorkA_LocalWorkMsgEPvP11WorkDistri > >b+0x12 [0x81896d2] [15] /usr/local/bin/namd2 [0x819e8b4] > > [16] /usr/local/bin/namd2 [0x819e97f] > > [17] _Z15_processHandlerPv+0x208 [0x819d8e0] > > [18] CmiHandleMessage+0x35 [0x81ca545] > > [19] CsdScheduleForever+0x64 [0x81ca6b8] > > [20] CsdScheduler+0x11 [0x81ca619] > > [21] _ZN7BackEnd4initEiPPc+0x96 [0x80b4f86] > > [22] main+0x1e [0x80b211e] > > [23] __libc_start_main+0xbb [0x4017317f] > > [24] log+0x79 [0x80ae711] > > Fatal error on PE 2> segmentation violation > > ****************************************************** > > configuration file: > > ********************************************* > > # NAMD configuration file for equilibration running of apbp in a 43A^3 > > DMSO box # the system has one apbp molecule and 645 DMSO molecules.2702 > > atoms totally # molecular system > > structure data/apb_dmso_xplor.psf > > coordinates crd/apb_min.pdb > > #periodic boundary condition > > cellbasisvector1 45.00 0 0 > > cellbasisvector2 0 45.00 0 > > cellbasisvector3 0 0 45.00 > > wrapall on > > #extended system > > #extendedsystem apb_cpt_boxsize.xsc > > xstfile apb_cpt_boxsize_traj.xst > > xstfreq 1000 > > # force field > > paratypecharmm on > > parameters data/apbdmso.prm > > exclude scaled1-4 > > 1-4scaling 1.0 > > # approximations > > switching on > > switchdist 8 > > cutoff 10 > > pairlistdist 12 > > stepspercycle 20 > > #pme > > pme on > > pmegridsizex 50 > > pmegridsizey 50 > > pmegridsizez 50 > > #NPT ENSEMBLE > > #Langevin dynamics > > langevin on # do langevin dynamics > > langevinDamping 5 # damping coefficient (gamma) of 5/ps > > langevinTemp 300 # bath temperature > > langevinHydrogen no # don't couple langevin bath to hydrogens > > # pressure > > langevinPiston on > > langevinPistonTarget 1.01325 # in bar -> 1 atm > > langevinPistonPeriod 100 > > langevinPistonDecay 50 > > langevinPistonTemp 300 > > useGroupPressure yes > > #integrator > > timestep 1.0 > > numsteps 500000 > > #output > > outputname apb_min > > binaryoutput no > > restartname apb_restart > > restartfreq 1000 > > #restartsave yes > > outputenergies 100 > > outputpressure 100 > > #multi-timestep parameters > > fullelectfrequency 2 > > #protocol > > temperature 300 > > #reassignFreq 10000 > > #reassignIncr 25 > > #reassignHold 300 > > #minimization on > > NAMD: Scalable Molecular Dynamics > http://www.ks.uiuc.edu/Research/namd/