From owner-chemistry@ccl.net Thu Jul 13 08:11:00 2006 From: "Jens Thomas j.m.h.thomas(-)dl.ac.uk" To: CCL Subject: CCL: Freezing angles in GAMESS-UK/CHARMM QM/MM simulations? Message-Id: <-32120-060713075128-30071-DJo1GWZe79Xwe0xyo9VyTQ++server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Jul 2006 12:14:43 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas .. dl.ac.uk] Dear James, It is possible to hold an angle or bond length constant in GAMESS-UK, provided that the molecule has been defined with a Z-matrix. If this is the case, then you can decide which of the bond lengths and angles are free to vary and those that are to be held constant. There is more information on this in the GAMESS-UK manual at: http://www.cfs.dl.ac.uk/docs/gamess_manual/chap3/node11.html If you don't have a Z-matrix definition for your molecule, than the freely available CCP1GUI has the ability to automatically construct a Z-matrix definition from Cartesian coordinates. You can find out more about the CCP1GUI at: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml Whether this is possible for QM/MM modelling depends on the QM/MM environment within which you are using GAMESS-UK. If that permits the QM region to be defined with a Z-matrix, or supports constraining certain bonds and angles itself, there should be no problem in keeping the relevant bonds and angles fixed. I hope this helps. Best wishes, Jens James N Scott scottjn],[gmail.com wrote: > Sent to CCL by: "James N Scott" [scottjn-$-gmail.com] > Greetings CCLers. I am on the verge of purchasing GAMESS-UK in order to do some simple QM/MM simulations of different small molecules in water, with the goal of examining solvent effects on spectra. > > Is it possible to make constant an angle or bond length internal to the QM system of interest? For instance, can I fix a dihedral angle between two QM molecules embedded in MM water molecules, or a bond length within a single QM molecule? > > Thanks very much for any assistance! > > J. Nathan Scott> > > > > > From owner-chemistry@ccl.net Thu Jul 13 10:12:01 2006 From: "Barry Hardy barry.hardy[#]tiscalinet.ch" To: CCL Subject: CCL: Poster Session & Submissions for eCheminfo Meeting, Bryn Mawr, 16-19 October Message-Id: <-32121-060713100943-15387-6oC/YDMDhytT9tkkR9jR1g=-=server.ccl.net> X-Original-From: Barry Hardy Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 13 Jul 2006 16:09:27 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy|*|tiscalinet.ch] We will hold a "traditional" poster session at the Autumn eCheminfo Meeting "Latest Advances in Drug Discovery Design & Planning Methods" which takes place 16-19 October 2006, Bryn Mawr, Philadelphia, USA Poster Abstracts (of ca. 300 words) with Title, Institution, Address, Authors and Contact Information should be submitted for review to eCheminfo [at] douglasconnect.com Poster Abstract submission deadline is 31 August 2006 although earlier submissions are encouraged. Posters may be on any topic of relevance to drug discovery and development but should include new or recent novel research, application or innovation. The meeting themes include Structure-based Drug Design, Screening & Docking, Cheminformatics & Modeling supporting Medicinal Chemistry, Pharmacophores, Metabolomics, Quantum Biochemistry, Knowledge Management, Electronic Lab Notebooks, Critical Path Innovation in Drug Development, Biomarkers, Predictive Toxicology & ADME. The poster session is planned to take place on the evening of Wednesday October 18th and will be accompanied by a bbq on campus. If we have too many posters for viewing that evening, we will also run a second evening on Monday October 16th. Open seminars and workshops on Electronic Lab Notebooks and a Knowledge Cafe on knowledge management in R&D will take place the afternoon & evening of October 17th. (Open for proposals through 21 July, please contact barry.hardy [at] douglasconnect.com to discuss program proposals). The preliminary main conference and workshop program and schedule for the meeting is available at: http://www.echeminfo.com/COMTY_conferences/ Registration enquiries can be directed to eCheminfo [at] douglasconnect.com best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Baermeggenweg 14, Zeiningen CH-4314, Switzerland Tel: +41 61 851 0170 Confirmed Speakers at the Bryn Mawr meeting include: Frank Hollinger (Locus Pharmaceuticals), Erin Duffy (Rib-X), Mike Malamas (Wyeth), Debananda Das (NCI), Max Cummings (Johnson & Johnson PR&D), Lance Westerhoff (QuantumBio), Jose Duca (Schering-Plough), Osman Guner (Turquoise Consulting), Hege Beard (Schrodinger), Stan Young (NISS), John Irwin (UCSF), William Douglas Figg (NCI), Darryl Reid (SimBioSys), Gregory Warren (GlaxoSmithKline), Deepak Bandyopadhyay (Johnson & Johnson PR&D), Paul Hawkins (OpenEye), Chris Cooper (BMS), James Arnold (Astra-Zeneca), Phil Edwards (Astra-Zeneca), Pete Connolly (Johnson & Johnson PR&D), Dimitris Agrafiotis (Johnson & Johnson PRD), Jim Wikel (Coalesix), Tudor Oprea (Univ. New Mexico), Alex Tropsha (UNC), Curt Breneman (RPI), Sanji Bhal (ACD/Labs), Michael Bolger (Simulations Plus), Bob Clark (Tripos), Gilles Klopman (Multicase), Navita Mallalieu (Roche Pharmaceuticals), Zentam Tsuchihashi (BMS), Peter Henstock (Pfizer), Darius Dziuda (Multivariate bioMarkers Discovery), Keith Elliston (Genstruct), Michael Liebman (Windber Research Institute), Jonathan Sheldon (InforSense), Duane Shugars (Concentia Digital), Jian Wang (Biofortis), Peter Gates (Johnson & Johnson PR&D), Barry Hardy (Douglas Connect), Dennis Underwood (Praxeon), Jeff Spitzner (Rescentris), David Mosenkis (Spotfire), Joel Hoffman (Insightful Corporation), Delia Wolf (Harvard Medical School), Craig Liddell (Realtime Science), Joseph Bitran (Enterprizer), Alvin Berger (Metabolon), Gregory Banik (Bio-RAD), George Harrigan (Monsanto), Rick Beger (NCTR, FDA), Don Robertson (Pfizer), Teresa Garret (Duke University), Laszlo Boros (SIDMAP), Bruce Kristal (Cornell University), Andrew Lane (JG Brown Cancer Center, U. Louisville), Oliver Fiehn (UC Davis Genome Center), Susan Connor (Glaxo SmithKline), Michael Jones (Novartis) From owner-chemistry@ccl.net Thu Jul 13 12:03:01 2006 From: "Pavel Starkov pavel.starkov*o*imperial.ac.uk" To: CCL Subject: CCL: AutoDock and ion charge Message-Id: <-32122-060713105128-23749-z8IrXOTAUBlwVEMiamJnNQ .. server.ccl.net> X-Original-From: "Pavel Starkov" Date: Thu, 13 Jul 2006 10:51:28 -0400 Sent to CCL by: "Pavel Starkov" [pavel.starkov .. imperial.ac.uk] Dear All, Could anyone have a suggestion how one might assign/change ion charge in AutoDock/ADT. Thank you in advance, Pavel Starkov MRes student in Biomolecular Science Imperial College London From owner-chemistry@ccl.net Thu Jul 13 14:35:00 2006 From: "Nathan Scott scottjn{:}gmail.com" To: CCL Subject: CCL: Freezing angles in GAMESS-UK/CHARMM QM/MM simulations? Message-Id: <-32123-060713143111-22315-J8kLAWlb7xpGIGKf7hY5yA.:.server.ccl.net> X-Original-From: "Nathan Scott" Content-Type: multipart/alternative; boundary="----=_Part_18445_11101932.1152812744491" Date: Thu, 13 Jul 2006 13:45:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Nathan Scott" [scottjn^-^gmail.com] ------=_Part_18445_11101932.1152812744491 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Jens, Can you (or anyone else) point me to a list of QM/MM environments that support the GAMESS-UK/CHARMM combination? I am aware of the ChemShell interface, but are there others? For what it's worth, the molecules I am interested in are fairly simple (less than 20 atoms), and I just want to solvate them with ~1000 TIP4P water molecules. I sincerely thank you for your help! J. Nathan Scott On 7/13/06, Jens Thomas j.m.h.thomas(-)dl.ac.uk wrote: > > Sent to CCL by: Jens Thomas [j.m.h.thomas .. dl.ac.uk] > Dear James, > > It is possible to hold an angle or bond length constant in GAMESS-UK, > provided that the molecule has been defined with a Z-matrix. If this is > the case, then you can decide which of the bond lengths and angles are > free to vary and those that are to be held constant. > > There is more information on this in the GAMESS-UK manual at: > > http://www.cfs.dl.ac.uk/docs/gamess_manual/chap3/node11.html > > If you don't have a Z-matrix definition for your molecule, than the > freely available CCP1GUI has the ability to automatically construct a > Z-matrix definition from Cartesian coordinates. > > You can find out more about the CCP1GUI at: > > http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml > > Whether this is possible for QM/MM modelling depends on the QM/MM > environment within which you are using GAMESS-UK. If that permits the QM > region to be defined with a Z-matrix, or supports constraining certain > bonds and angles itself, there should be no problem in keeping the > relevant bonds and angles fixed. > > I hope this helps. > > Best wishes, > > Jens > > James N Scott scottjn],[gmail.com wrote: > > Sent to CCL by: "James N Scott" [scottjn-$-gmail.com] > > Greetings CCLers. I am on the verge of purchasing GAMESS-UK in order to > do some simple QM/MM simulations of different small molecules in water, with > the goal of examining solvent effects on spectra. > > > > Is it possible to make constant an angle or bond length internal to the > QM system of interest? For instance, can I fix a dihedral angle between two > QM molecules embedded in MM water molecules, or a bond length within a > single QM molecule? > > > > Thanks very much for any assistance! > > > > J. Nathan Scott> > > > ------=_Part_18445_11101932.1152812744491 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Jens,

Can you (or anyone else) point me to a list of QM/MM environments that support the GAMESS-UK/CHARMM combination?  I am aware of the ChemShell interface, but are there others?  For what it's worth, the molecules I am interested in are fairly simple (less than 20 atoms), and I just want to solvate them with ~1000 TIP4P water molecules.

I sincerely thank you for your help!

J. Nathan Scott

On 7/13/06, Jens Thomas j.m.h.thomas(-)dl.ac.uk < owner-chemistry+*+ccl.net> wrote:
Sent to CCL by: Jens Thomas [j.m.h.thomas .. dl.ac.uk]
Dear James,

It is possible to hold an angle or bond length constant in GAMESS-UK,
provided that the molecule has been defined with a Z-matrix. If this is
the case, then you can decide which of the bond lengths and angles are
free to vary and those that are to be held constant.

There is more information on this in the GAMESS-UK manual at:

http://www.cfs.dl.ac.uk/docs/gamess_manual/chap3/node11.html

If you don't have a Z-matrix definition for your molecule, than the
freely available CCP1GUI has the ability to automatically construct a
Z-matrix definition from Cartesian coordinates.

You can find out more about the CCP1GUI at:

http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml

Whether this is possible for QM/MM modelling depends on the QM/MM
environment within which you are using GAMESS-UK. If that permits the QM
region to be defined with a Z-matrix, or supports constraining certain
bonds and angles itself, there should be no problem in keeping the
relevant bonds and angles fixed.

I hope this helps.

Best wishes,

Jens

James N Scott scottjn],[gmail.com wrote:
> Sent to CCL by: "James N Scott" [scottjn-$-gmail.com]
> Greetings CCLers.  I am on the verge of purchasing GAMESS-UK in order to do some simple QM/MM simulations of different small molecules in water, with the goal of examining solvent effects on spectra.
>
> Is it possible to make constant an angle or bond length internal to the QM system of interest?  For instance, can I fix a dihedral angle between two QM molecules embedded in MM water molecules, or a bond length within a single QM molecule?
>
> Thanks very much for any assistance!
>
> J. Nathan Scott>
>
>
>
>
>



E-mail to subscribers: CHEMISTRY+*+ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST+*+ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
      

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig   (login: ccl, Password: search)
      http://www.ccl.net/spammers.txt

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




------=_Part_18445_11101932.1152812744491-- From owner-chemistry@ccl.net Thu Jul 13 15:37:00 2006 From: "Miklos Vargyas miklos.vargyas[-]chemaxon.hu" To: CCL Subject: CCL: RXN to SMIRKS Message-Id: <-32124-060713153503-4754-/7BjtPAmPZ+aWRFAFqwNAQ,,server.ccl.net> X-Original-From: "Miklos Vargyas" Date: Thu, 13 Jul 2006 15:34:59 -0400 Sent to CCL by: "Miklos Vargyas" [miklos.vargyas%x%chemaxon.hu] Dear Didier, MolConverter can convert RXN files into SMIRKS. It can batch process reaction files. However, if you need an application with a GUI, then you can use MarvinSketch. Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html. The MolConverter application (as well as MarvinSketch, MarvinView and MarvinSpace) are free for all users if they are not used as integral parts of other applications. The MolConverter application (http://www.chemaxon.com/marvin/doc/user/molconvert.html) is available in the Marvin Beans package that can be dowloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/) Best regards, Miklos Miklos Vargyas, PhD ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3670 3813205 Tel: +361 4532661 Skype: miklos.vargyas Fax: +361 4532659 e-mail: mvargyas]=[chemaxon.com Didier ROGNAN didier.rognan{}pharma.u-strasbg.fr wrote: >Sent to CCL by: "Didier ROGNAN" [didier.rognan(-)pharma.u-strasbg.fr] >Dear colleagues, > > > >Has anyone a free routine able to convert a MDL rxn file into SMIRKS ? > > > >Many thanks for your answer > >Kind regards > >------------------------------------------------------------------------------\----------------- >Dr. Didier ROGNAN >Directeur de Recherche >CNRS UMR 7175-LC1 >Institut Gilbert-Laustriat >74, route du Rhin, B.P.24 >F-67401 Illkirch From owner-chemistry@ccl.net Thu Jul 13 16:29:01 2006 From: "Boyd, D. boyd]-[chem.iupui.edu" To: CCL Subject: CCL: Gordon Conference in October Message-Id: <-32125-060713161541-16428-3u75LiEG5MHT0i7ESU46DA*o*server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Jul 2006 15:09:13 -0400 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd~!~chem.iupui.edu] Where can you combine the latest in molecular modeling and simulations research with incomparable Swiss mountain scenery? The 2006 Gordon Research Conference on Computational Chemistry will be held 8-13 October 2006 in Les Diablerets, Switzerland. For more information, see http://chem.iupui.edu/rcc/grccc.html and www.grc.org Register soon. The conference is filling up. Don From owner-chemistry@ccl.net Thu Jul 13 17:03:00 2006 From: "Samuel C Flores samuel.flores^-^yale.edu" To: CCL Subject: CCL: hmm.. how about expl solvent? RE: accounting for counterions in implicit solvent? Message-Id: <-32126-060713162802-20359-Ao4JARpL9utWT1GPLSlehA:server.ccl.net> X-Original-From: "Samuel C Flores" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 13 Jul 2006 16:27:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Samuel C Flores" [samuel.flores**yale.edu] Hmm.. very good. I will look into this. Implementing such a code could be an interesting exercise. Another question: If I use explicit solvent, do you think it is sufficient to add enough counterions to balance the net charge, or do I need to look at the molecular surface carefully and make sure each charged surface residue has a neutralizing charge? I think the latter will end up generating a whole bunch of counterions, for MurA. I am using GROMACS for the explicit solvent version of my code and don't know if GROMACS has code to do this automatically, as I understand Amber's CION does. Sam -----Original Message----- > From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net] Sent: Wednesday, July 12, 2006 2:34 PM To: Flores, Samuel Subject: CCL: accounting for counterions in implicit solvent? Sent to CCL by: "David A. Case" [case===scripps.edu] On Tue, Jul 11, 2006, Samuel C Flores samuel.flores^^yale.edu wrote: > > Is there an implicit solvent code available that takes into account the > effect of counterions? I have several positive charges in my protein, so if > I use plain vanilla implicit solvent models in TINKER, the protein denatures > slightly. I would prefer to use TINKER or CHARMm, but will consider other > academic codes. One simple approach to this problem is given here: %A J. Srinivasan %A M.W. Trevathan %A P. Beroza %A D.A. Case %T Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects %J Theor. Chem. Acc. %V 101 %P 426-434 %D 1999 This idea is implemented in Amber and NAB; it is also in CHARMM, but perhaps not yet in any released version. Since the idea is so simple, it is probably easy to add it to TINKER or to other implicit solvent codes. Note also that it has not really been critically tested: at best, it will mimic adding Debye-Huckel screening in a linearlized Poisson-Boltzman approach. So, use with caution. ..hope this helps...dave casehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jul 13 17:33:59 2006 From: "Pavel Starkov pavel.starkov..imperial.ac.uk" To: CCL Subject: CCL: AutoDock and ion charge Message-Id: <-32128-060713105128-23749-ING1h3kG2RvetexbP8L6YA**server.ccl.net> X-Original-From: "Pavel Starkov" Date: Thu, 13 Jul 2006 10:51:28 -0400 Sent to CCL by: "Pavel Starkov" [pavel.starkov/./imperial.ac.uk] Dear All, Could anyone have a suggestion how one might assign/change ion charge in AutoDock/ADT. Thank you in advance, Pavel Starkov MRes student in Biomolecular Science Imperial College London From owner-chemistry@ccl.net Thu Jul 13 17:31:40 2006 From: "Pavel Starkov pavel.starkov+/-imperial.ac.uk" To: CCL Subject: CCL: AutoDock and ion charge Message-Id: <-32127-060713105128-23749-qShz1YcrWhzYeMTdX9eKRQ]![server.ccl.net> X-Original-From: "Pavel Starkov" Date: Thu, 13 Jul 2006 10:51:28 -0400 Sent to CCL by: "Pavel Starkov" [pavel.starkov(~)imperial.ac.uk] Dear All, Could anyone have a suggestion how one might assign/change ion charge in AutoDock/ADT. Thank you in advance, Pavel Starkov MRes student in Biomolecular Science Imperial College London From owner-chemistry@ccl.net Thu Jul 13 20:03:58 2006 From: "Samuel C Flores samuel.flores!=!yale.edu" To: CCL Subject: CCL: hmm.. how about expl solvent? RE: accounting for counterions in implicit solvent? Message-Id: <-32134-060713162802-20359-uW8tJsodiG5mKwm9lWnHFA]=[server.ccl.net> X-Original-From: "Samuel C Flores" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 13 Jul 2006 16:27:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Samuel C Flores" [samuel.flores]*[yale.edu] Hmm.. very good. I will look into this. Implementing such a code could be an interesting exercise. Another question: If I use explicit solvent, do you think it is sufficient to add enough counterions to balance the net charge, or do I need to look at the molecular surface carefully and make sure each charged surface residue has a neutralizing charge? I think the latter will end up generating a whole bunch of counterions, for MurA. I am using GROMACS for the explicit solvent version of my code and don't know if GROMACS has code to do this automatically, as I understand Amber's CION does. Sam -----Original Message----- > From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] Sent: Wednesday, July 12, 2006 2:34 PM To: Flores, Samuel Subject: CCL: accounting for counterions in implicit solvent? Sent to CCL by: "David A. Case" [case===scripps.edu] On Tue, Jul 11, 2006, Samuel C Flores samuel.flores^^yale.edu wrote: > > Is there an implicit solvent code available that takes into account the > effect of counterions? I have several positive charges in my protein, so if > I use plain vanilla implicit solvent models in TINKER, the protein denatures > slightly. I would prefer to use TINKER or CHARMm, but will consider other > academic codes. One simple approach to this problem is given here: %A J. Srinivasan %A M.W. Trevathan %A P. Beroza %A D.A. Case %T Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects %J Theor. Chem. Acc. %V 101 %P 426-434 %D 1999 This idea is implemented in Amber and NAB; it is also in CHARMM, but perhaps not yet in any released version. Since the idea is so simple, it is probably easy to add it to TINKER or to other implicit solvent codes. Note also that it has not really been critically tested: at best, it will mimic adding Debye-Huckel screening in a linearlized Poisson-Boltzman approach. So, use with caution. ..hope this helps...dave casehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jul 13 20:01:05 2006 From: "Nathan Scott scottjn~!~gmail.com" To: CCL Subject: CCL: Freezing angles in GAMESS-UK/CHARMM QM/MM simulations? Message-Id: <-32131-060713143111-22315-B51bRfV6M1mjK1tKasKdzw=-=server.ccl.net> X-Original-From: "Nathan Scott" Content-Type: multipart/alternative; boundary="----=_Part_18445_11101932.1152812744491" Date: Thu, 13 Jul 2006 13:45:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Nathan Scott" [scottjn*o*gmail.com] ------=_Part_18445_11101932.1152812744491 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Jens, Can you (or anyone else) point me to a list of QM/MM environments that support the GAMESS-UK/CHARMM combination? I am aware of the ChemShell interface, but are there others? For what it's worth, the molecules I am interested in are fairly simple (less than 20 atoms), and I just want to solvate them with ~1000 TIP4P water molecules. I sincerely thank you for your help! J. Nathan Scott On 7/13/06, Jens Thomas j.m.h.thomas(-)dl.ac.uk wrote: > > Sent to CCL by: Jens Thomas [j.m.h.thomas .. dl.ac.uk] > Dear James, > > It is possible to hold an angle or bond length constant in GAMESS-UK, > provided that the molecule has been defined with a Z-matrix. If this is > the case, then you can decide which of the bond lengths and angles are > free to vary and those that are to be held constant. > > There is more information on this in the GAMESS-UK manual at: > > http://www.cfs.dl.ac.uk/docs/gamess_manual/chap3/node11.html > > If you don't have a Z-matrix definition for your molecule, than the > freely available CCP1GUI has the ability to automatically construct a > Z-matrix definition from Cartesian coordinates. > > You can find out more about the CCP1GUI at: > > http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml > > Whether this is possible for QM/MM modelling depends on the QM/MM > environment within which you are using GAMESS-UK. If that permits the QM > region to be defined with a Z-matrix, or supports constraining certain > bonds and angles itself, there should be no problem in keeping the > relevant bonds and angles fixed. > > I hope this helps. > > Best wishes, > > Jens > > James N Scott scottjn],[gmail.com wrote: > > Sent to CCL by: "James N Scott" [scottjn-$-gmail.com] > > Greetings CCLers. I am on the verge of purchasing GAMESS-UK in order to > do some simple QM/MM simulations of different small molecules in water, with > the goal of examining solvent effects on spectra. > > > > Is it possible to make constant an angle or bond length internal to the > QM system of interest? For instance, can I fix a dihedral angle between two > QM molecules embedded in MM water molecules, or a bond length within a > single QM molecule? > > > > Thanks very much for any assistance! > > > > J. Nathan Scott> > > > ------=_Part_18445_11101932.1152812744491 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Jens,

Can you (or anyone else) point me to a list of QM/MM environments that support the GAMESS-UK/CHARMM combination?  I am aware of the ChemShell interface, but are there others?  For what it's worth, the molecules I am interested in are fairly simple (less than 20 atoms), and I just want to solvate them with ~1000 TIP4P water molecules.

I sincerely thank you for your help!

J. Nathan Scott

On 7/13/06, Jens Thomas j.m.h.thomas(-)dl.ac.uk < owner-chemistry*ccl.net> wrote:
Sent to CCL by: Jens Thomas [j.m.h.thomas .. dl.ac.uk]
Dear James,

It is possible to hold an angle or bond length constant in GAMESS-UK,
provided that the molecule has been defined with a Z-matrix. If this is
the case, then you can decide which of the bond lengths and angles are
free to vary and those that are to be held constant.

There is more information on this in the GAMESS-UK manual at:

http://www.cfs.dl.ac.uk/docs/gamess_manual/chap3/node11.html

If you don't have a Z-matrix definition for your molecule, than the
freely available CCP1GUI has the ability to automatically construct a
Z-matrix definition from Cartesian coordinates.

You can find out more about the CCP1GUI at:

http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml

Whether this is possible for QM/MM modelling depends on the QM/MM
environment within which you are using GAMESS-UK. If that permits the QM
region to be defined with a Z-matrix, or supports constraining certain
bonds and angles itself, there should be no problem in keeping the
relevant bonds and angles fixed.

I hope this helps.

Best wishes,

Jens

James N Scott scottjn],[gmail.com wrote:
> Sent to CCL by: "James N Scott" [scottjn-$-gmail.com]
> Greetings CCLers.  I am on the verge of purchasing GAMESS-UK in order to do some simple QM/MM simulations of different small molecules in water, with the goal of examining solvent effects on spectra.
>
> Is it possible to make constant an angle or bond length internal to the QM system of interest?  For instance, can I fix a dihedral angle between two QM molecules embedded in MM water molecules, or a bond length within a single QM molecule?
>
> Thanks very much for any assistance!
>
> J. Nathan Scott>
>
>
>
>
>



E-mail to subscribers: CHEMISTRY*ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
      

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig   (login: ccl, Password: search)
      http://www.ccl.net/spammers.txt

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




------=_Part_18445_11101932.1152812744491-- From owner-chemistry@ccl.net Thu Jul 13 20:01:46 2006 From: "Miklos Vargyas miklos.vargyas=chemaxon.hu" To: CCL Subject: CCL: RXN to SMIRKS Message-Id: <-32132-060713153503-4754-/XpCIFhiSbd64I78zd8lHw%server.ccl.net> X-Original-From: "Miklos Vargyas" Date: Thu, 13 Jul 2006 15:34:59 -0400 Sent to CCL by: "Miklos Vargyas" [miklos.vargyas__chemaxon.hu] Dear Didier, MolConverter can convert RXN files into SMIRKS. It can batch process reaction files. However, if you need an application with a GUI, then you can use MarvinSketch. Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html. The MolConverter application (as well as MarvinSketch, MarvinView and MarvinSpace) are free for all users if they are not used as integral parts of other applications. The MolConverter application (http://www.chemaxon.com/marvin/doc/user/molconvert.html) is available in the Marvin Beans package that can be dowloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/) Best regards, Miklos Miklos Vargyas, PhD ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3670 3813205 Tel: +361 4532661 Skype: miklos.vargyas Fax: +361 4532659 e-mail: mvargyas#%#chemaxon.com Didier ROGNAN didier.rognan{}pharma.u-strasbg.fr wrote: >Sent to CCL by: "Didier ROGNAN" [didier.rognan(-)pharma.u-strasbg.fr] >Dear colleagues, > > > >Has anyone a free routine able to convert a MDL rxn file into SMIRKS ? > > > >Many thanks for your answer > >Kind regards > >------------------------------------------------------------------------------\----------------- >Dr. Didier ROGNAN >Directeur de Recherche >CNRS UMR 7175-LC1 >Institut Gilbert-Laustriat >74, route du Rhin, B.P.24 >F-67401 Illkirch From owner-chemistry@ccl.net Thu Jul 13 20:03:28 2006 From: "Boyd, D. boyd#chem.iupui.edu" To: CCL Subject: CCL: Gordon Conference in October Message-Id: <-32133-060713161541-16428-+4ZjaptIjBvKQ6Z7i0CcvQ!=!server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Jul 2006 15:09:13 -0400 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd-.-chem.iupui.edu] Where can you combine the latest in molecular modeling and simulations research with incomparable Swiss mountain scenery? The 2006 Gordon Research Conference on Computational Chemistry will be held 8-13 October 2006 in Les Diablerets, Switzerland. For more information, see http://chem.iupui.edu/rcc/grccc.html and www.grc.org Register soon. The conference is filling up. Don