From owner-chemistry@ccl.net Thu Apr 9 02:39:00 2009 From: "alexandra.marques.|*|.fc.up.pt" To: CCL Subject: CCL: transition states of enzymes Message-Id: <-39041-090408185956-10380-1ClQb8qIXk3bzTxxvhHrzQ|*|server.ccl.net> X-Original-From: alexandra.marques|fc.up.pt Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 09 Apr 2009 00:04:07 +0200 MIME-Version: 1.0 Sent to CCL by: alexandra.marques=-=fc.up.pt Hi, I have been read some articles about the search for transitions state structures in enzymatic reactions but I still have some doubts: 1) It seems that when the full enzyme is intended to be used the most widely used approach is to use QM/MM to model the enzyme and perform a relaxed PES scan along some reaction coordinate. Is this correct or there are better methods? 2) Imagining that an approximate transition state can be identified in a PES scan with the full enzyme, then, which method shall be used to prove that this is the correct transition state? I am asking that because I think a frequency calculation or even the IRC method cannot be applied for a large system? Can anyone help me please. Thanks a lot Alexandra ------------------------------------------------------------------------- A FCUP utiliza o sistema open source de webmail Horde/IMP (www.horde.org) Visite: http://www.fc.up.pt/ http://info.fc.up.pt/ From owner-chemistry@ccl.net Thu Apr 9 05:41:01 2009 From: "Arvydas Tamulis tamulis . itpa.lt" To: CCL Subject: CCL:G: Comparison with G03 Message-Id: <-39042-090409044247-29650-djpA+acKU4skj8alUb10wA%x%server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Thu, 9 Apr 2009 10:57:46 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis(a)itpa.lt] Dear Colleagues, maybe somebody can run for me one single point calculation using G03 for comparison with my done calculations with TURBOMOLE, ORCA and GAMESS-US: #P B3LYP/6-31+G(d) IOp(6/12=3) SCF=tight DIIS Pop=Full Guanine-Cytosine stacking with 101 H2O molecules after PM3 optimization 0 1 n c 1 cn2 c 2 cc3 1 ccn3 n 3 nc4 2 ncc4 1 dih4 ... Thanking your in advance. With best regards, Arvydas http://www.itpa.lt/~tamulis/ From owner-chemistry@ccl.net Thu Apr 9 06:09:00 2009 From: "FyD fyd%q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Release of R.E.D. Server Message-Id: <-39043-090409052606-30202-dRlXl89DXBtL303uPW76oA%%server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 09 Apr 2009 10:31:30 +0200 MIME-Version: 1.0 Sent to CCL by: FyD [fyd]*[q4md-forcefieldtools.org] Dear All, I am pleased to announce the release of R.E.D. Server available * =20 http://q4md-forcefieldtools.org/REDS/. R.E.D. Server provides the software and hardware (i. e. a cluster of =20 computers) required for the derivation of highly effective and =20 reproducible RESP and ESP atomic charge values embedded in force field =20 libraries suitable for molecular dynamics simulations. R.E.D. Server =20 interfaces the last stable version of the RESP ESP charge Derive =20 program (R.E.D. IV April 2009 so far) developed by the q4md force =20 field tools team, and provides the binaries for the last versions of =20 the Gaussian, GAMESS-US, or the PC-GAMESS/Firefly program, and for the =20 RESP program. More generally, the last developments in term of RESP =20 and ESP charge derivation carried out by the q4md force field tools =20 team will be provided through R.E.D. Server. The release of these new =20 developments will be carried out from time to time, and the =20 description of those last features released in R.E.D. Server is =20 available at the "R.E.D. Server news" web page. By involving multiple molecules, multiple conformations and multiple =20 orientations in charge derivation and by handling specific charge =20 constraints during the fitting step, R.E.D. IV allows building complex =20 force field topology database or FFTopDB corresponding to the =20 simultaneous generation of numerous molecular fragments (N-terminal, =20 C-terminal and central amino acid fragments, 5'- or Y'-terminal, 3'- =20 or X'-terminal and central nucleotide fragments as well as =20 monosaccharide and metal complex fragments) in a single execution. The =20 all atom or united-carbon force field library model can be =20 in-differentially generated. A procedure to study the impact of the =20 various charge constraints required during the fitting step of a =20 molecular fragment has been implemented allowing users to compare =20 charge values, and thus to validate or reject charge sets. The use of R.E.D. Server and R.E.D. IV is described in Frequently =20 Asked Questions http://q4md-forcefieldtools.org/REDS/faq.php as well =20 as in a specific tutorial =20 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php. Academic users involved in non-profit research are authorized to use =20 R.E.D. Server. The use of R.E.D. Server is provided at no cost after =20 signing a license agreement. The PI (principal investigator or =20 Director of a laboratory) and the PU (R.E.D. Server principal user) =20 have to register and sign a license agreement to be authorized to use =20 R.E.D. Server. A general public help is provided with the q4md-forcefieldtools =20 mailing list. Any researcher can participate in this mailing list by =20 answering and/or sending queries at q4md-fft*q4md-forcefieldtools.org =20 after registration at sympa*q4md-forcefieldtools.org. Archives of the =20 q4md-fft mailing list are public. A private assistance is also =20 available for registered users from the "Assistance" Service available =20 at the R.E.D. Server Home page. We are registered in the AMBER and CCL =20 mailing lists, and we will answer to the queries about the q4md force =20 field tools in these mailing lists as well. The R.E.D. III.2 tools distributed in a standalone version at =20 http://q4md-forcefieldtools.org/RED/, the RESP ESP charge DDataBase =20 (or R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/) which allows =20 freely storing and distributing RESP and ESP charges embedded in force =20 field libraries in the scientific community and R.E.D. Server =20 constitute to the best of our knowledge unique tools. regards, F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ From owner-chemistry@ccl.net Thu Apr 9 06:43:01 2009 From: "V ronique LEGRAND vflegrand^_^free.fr" To: CCL Subject: CCL: orbital permutation Message-Id: <-39044-090409063415-4155-2K6MI2y5FnJK2RVgDNskvA ~~ server.ccl.net> X-Original-From: "V ronique LEGRAND" Date: Thu, 9 Apr 2009 06:34:10 -0400 Sent to CCL by: "V ronique LEGRAND" [vflegrand,+,free.fr] Hello every body, I have to permute some orbitals to build a radical in the correct way. I suceeded to reorganize the orbitals (the ouput list them correctly). But I decided to check it with an NBO analysis, to be sure the occupancy of orbitals are really what I want. But it was like I made no permutation at all. I realized my permutation like this: #P UB3LYP/6-311+G(d,p) guess=(permute) scf =(tight) title 0 2 molecule description 1-401,556-577,424-555,402-423,578-891 1-401,556-577,424-555,402-423,578-891 Then I tried to take the checkpoint of the permutation and make an NBO on it : #P UB3LYP/6-311+G(d,p) SP GFPrint GFinput Guess=read geom=check GFinput Scf=Tight iop(5/14=2) Maxdisk=50000000 Pop=(Full,NBO)Test I tried also to perform the permutation and the NBO in the same time: #P UB3LYP/6-311+G(d,p) SP guess=(permute) GFPrint GFinput Scf=Tight iop(5/14=2) Maxdisk=50000000 Pop=(Full,NBO)Test or #P UB3LYP/6-311+G(d,p) guess=(permute,cards) GFPrint GFinput Scf=Tight iop(5/14=2) Maxdisk=50000000 Pop=(Full,NBO)Test The results of orbitals occupancy show me the permutation wasn't done. My molecule is like at the begin when the permutation wasn't already done. If someone could tell me how to check if a permutation was really performed. Thanks a lot in advance Veronique L From owner-chemistry@ccl.net Thu Apr 9 07:18:00 2009 From: "David Gallagher gallagher.da,,gmail.com" To: CCL Subject: CCL: transition states of enzymes Message-Id: <-39045-090409065547-24346-l3HXqVfz85jSYuyRUniL6g#server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 09 Apr 2009 02:38:06 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da=gmail.com] Hi Alexandra, An alternative approach to modelling transition states for enzymes, is the new MOPAC2009 with the linear scaling algorithm (Mozyme) and PM6. Mozyme allows for optimizations and transition state searches on entire systems of up to about 15,000 atoms. The new PM6 method was developed primarily for biological systems and calibrated partly with DFT structures, so it gives better geometries than the older semiempirical methods such as PM3 and AM1. Typically, semiempirical methods overestimate activation energies, however, they can be useful for relative numbers and trends (or even quantitative estimates with appropriate calibration), and starting geometries for higher level calculations. The bibliography at http://www.cacheresearch.com/mopac.html#mopac-support lists at least one paper on the applicability of MOPAC2009 to modelling transition states of enzymes. Another paper on hydrogen bonding in some amino acid systems, concludes that PM6 compares favorably with higher-level methods. Regards, David Gallagher CACheResearch.com At 03:04 PM 4/8/2009, alexandra.marques....fc.up.pt wrote: >Sent to CCL by: alexandra.marques=-=fc.up.pt >Hi, > >I have been read some articles about the search for transitions state >structures in enzymatic reactions but I still have some doubts: >1) It seems that when the full enzyme is intended to be used the most >widely used approach is to use QM/MM to model the enzyme and perform a >relaxed PES scan along some reaction coordinate. Is this correct or >there are better methods? >2) Imagining that an approximate transition state can be identified in >a PES scan with the full enzyme, then, which method shall be used to >prove that this is the correct transition state? I am asking that >because I think a frequency calculation or even the IRC method cannot >be applied for a large system? >Can anyone help me please. >Thanks a lot >Alexandra From owner-chemistry@ccl.net Thu Apr 9 08:38:00 2009 From: "zoran matovic zmatovic**kg.ac.yu" To: CCL Subject: CCL:G: Comparison with G03 Message-Id: <-39046-090409082548-22602-fsHEPFm9WwaJ/i0gKnUGVw ~ server.ccl.net> X-Original-From: "zoran matovic" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 9 Apr 2009 13:38:13 +0200 MIME-Version: 1.0 Sent to CCL by: "zoran matovic" [zmatovic+*+kg.ac.yu] Arvydas You have to provide correct gaussian input file allowing users to do g03 sp. This one doesn't include all structural data. zoran > #P B3LYP/6-31+G(d) IOp(6/12=3) SCF=tight DIIS Pop=Full > > Guanine-Cytosine stacking with 101 H2O molecules after PM3 optimization > > 0 1 > n > c 1 cn2 > c 2 cc3 1 ccn3 > n 3 nc4 2 ncc4 1 dih4 ... ----- Original Message ----- > From: "Arvydas Tamulis tamulis . itpa.lt" To: "Matovic, Zoran D " Sent: Thursday, April 09, 2009 09:57 Subject: CCL:G: Comparison with G03 > > Sent to CCL by: Arvydas Tamulis [tamulis(a)itpa.lt] > Dear Colleagues, > > maybe somebody can run for me one single point calculation using G03 for > comparison with my done calculations with TURBOMOLE, ORCA and GAMESS-US: > > #P B3LYP/6-31+G(d) IOp(6/12=3) SCF=tight DIIS Pop=Full > > Guanine-Cytosine stacking with 101 H2O molecules after PM3 optimization > > 0 1 > n > c 1 cn2 > c 2 cc3 1 ccn3 > n 3 nc4 2 ncc4 1 dih4 ... > > Thanking your in advance. > With best regards, > Arvydas > http://www.itpa.lt/~tamulis/> -------------------------------------------------------------------------------- No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.285 / Virus Database: 270.11.48/2048 - Release Date: 04/08/09 19:02:00 From owner-chemistry@ccl.net Thu Apr 9 09:13:01 2009 From: "muhavini cleophas wawire muhavini~~yahoo.com" To: CCL Subject: CCL:G: Ruthenium parameters into Gaussian zindo calculations Message-Id: <-39047-090409064839-17431-OGxx4Xkhwe3OfkUx/5rkeQ++server.ccl.net> X-Original-From: "muhavini cleophas wawire" Date: Thu, 9 Apr 2009 06:48:36 -0400 Sent to CCL by: "muhavini cleophas wawire" [muhavini(-)yahoo.com] Could someone kindly help me to understand how to introduce Ruthenium parameters into Gaussian Zindo calculations? Thanks. Muhavini cleophas From owner-chemistry@ccl.net Thu Apr 9 09:48:00 2009 From: "Moreau Yohann yohann.moreau.^^^.lcp.u-psud.fr" To: CCL Subject: CCL: transition states of enzymes Message-Id: <-39048-090409060053-8171-LDunhSfTTEZ+CigbSnRioQ^^^server.ccl.net> X-Original-From: Moreau Yohann Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 9 Apr 2009 11:15:10 +0200 MIME-Version: 1.0 Sent to CCL by: Moreau Yohann [yohann.moreau..lcp.u-psud.fr] Hi, Alexandra,=20 Here's my 2cents : QM/MM methods are widely used so as to take into account all the environme= nt=20 effects on the active site and the reaction. If you wish to study a particular reaction, you have to (once you have=20 obtained your structure) define an active part. This part includes all the= =20 atoms described by QM (but not only) and is of course located at the active= =20 site of your enzyme. The remaining atoms (i.e. the "non-active" part) are=20 frozen during all the following calculations (this is environment). Performing a PES scan is then possible by letting the active part to relax= =20 "around" the coordinate you explore. The active part is supposed not to cha= nge=20 drastically of shape during the scan, provided you already optimised it bef= ore=20 (which ensures you start from a -at least local- minimum of the PES). If you perform a scan with sufficiently small steps, the highest step in=20 energy will give you a quite good idea about the barrier height you wish to= =20 determine as it can give you a good idea of the transition structure. Starting from this point, you can look for the TS. If your active part is=20 small enough, you can compute the hessian of the active part in the field o= f=20 environment directly and then go on with usual TS search algorithms.=20 If your active part is large (this is generally the case) you should perfor= m=20 calculations on a reduced set of atoms, including the very few ones directl= y=20 involved in the reaction. This can work very well if you starts from a=20 structure you know to be very similar to the TS. You have to choose the goo= d=20 atoms. To make a clear answer to your question : characterising a TS in an enzymat= ic=20 reaction is feasible and of course important. You will be interested by onl= y=20 few frequencies if not only (the imaginary) one, the remaining ones should = not=20 be relevant. I would add, that, using the static approach used for studying the reactivi= ty=20 of enzymes by the mean of QM/MM, computing frequencies for the whole system= is=20 totally meaningless, of course. My answer is quite long, however, I hope this will help you. Best regards,=20 Yohann : > Sent to CCL by: alexandra.marques=3D-=3Dfc.up.pt > Hi, > > I have been read some articles about the search for transitions state > structures in enzymatic reactions but I still have some doubts: > 1) It seems that when the full enzyme is intended to be used the most > widely used approach is to use QM/MM to model the enzyme and perform a > relaxed PES scan along some reaction coordinate. Is this correct or > there are better methods? > 2) Imagining that an approximate transition state can be identified in > a PES scan with the full enzyme, then, which method shall be used to > prove that this is the correct transition state? I am asking that > because I think a frequency calculation or even the IRC method cannot > be applied for a large system? > Can anyone help me please. > Thanks a lot > Alexandra > > > ------------------------------------------------------------------------- > A FCUP utiliza o sistema open source de webmail Horde/IMP (www.horde.org) > Visite: http://www.fc.up.pt/ http://info.fc.up.pt/ > > > =2D-=20 Yohann Moreau Laboratoire de Chimie Physique Universit=E9 de Paris-Sud B=E2timent 349 91405 Orsay cedex =46rance Tel : +33 (0) 1 69 15 73 98 =46ax :+33 (0) 1 69 15 61 88 From owner-chemistry@ccl.net Thu Apr 9 10:33:00 2009 From: "neeraj misra neerajmisra[]hotmail.com" To: CCL Subject: CCL: nanocluster Message-Id: <-39049-090409103146-10651-BcdEKFoDuHzNaMyqVsNQCg##server.ccl.net> X-Original-From: "neeraj misra" Date: Thu, 9 Apr 2009 10:31:42 -0400 Sent to CCL by: "neeraj misra" [neerajmisra^-^hotmail.com] I shall be extremely thankful to anyone who suggests me any series of elements or system whose cluster can be modelled and studied for its structure,stability and energetics. From owner-chemistry@ccl.net Thu Apr 9 15:36:01 2009 From: "Mike Clark mike.clark28#%#yahoo.co.uk" To: CCL Subject: CCL:G: Fixing coordinate system in Gaussian Message-Id: <-39050-090409115357-1711-Y2rcXl1SFYz+0EnSu9e9jw]|[server.ccl.net> X-Original-From: "Mike Clark" Date: Thu, 9 Apr 2009 11:53:53 -0400 Sent to CCL by: "Mike Clark" [mike.clark28{}yahoo.co.uk] Hi all I am trying to do a single point calculation in Gaussian, the input is in cartesian coordinates, but the definition for the coordinate system are translated/rotated in the results file, is there anyway to force gaussian to use the fix input coordinates, while its possible to convert the results to the origin coordinates its just seems alot of unnecessary work, there must be an easier way to do this. Best Mike Clark From owner-chemistry@ccl.net Thu Apr 9 16:57:00 2009 From: "Duy Le ttduyle ~ gmail.com" To: CCL Subject: CCL:G: Fixing coordinate system in Gaussian Message-Id: <-39051-090409165410-8651-kSKO6enKpedwKe585aHRQA{=}server.ccl.net> X-Original-From: Duy Le Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 9 Apr 2009 16:53:38 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle**gmail.com] It is better this way so that Gaussian can improve speed of calculation due to some needed geometry operations. Writing a tiny code to translate it (if necessary) will be the cheaper. :-) On Thu, Apr 9, 2009 at 11:53 AM, Mike Clark mike.clark28#%#yahoo.co.uk wrote: > > Sent to CCL by: "Mike =A0Clark" [mike.clark28{}yahoo.co.uk] > Hi all > > I am trying to do a single point calculation in Gaussian, the input is in= cartesian coordinates, but the definition for the coordinate system are tr= anslated/rotated in the results file, is there anyway to force gaussian to = use the fix input coordinates, while its possible to convert the results to= the origin coordinates its just seems alot of unnecessary work, there must= be an easier way to do this. > > Best > > Mike Clark > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Men don't need hands to do things! From owner-chemistry@ccl.net Thu Apr 9 17:31:00 2009 From: "Duy Le ttduyle(-)gmail.com" To: CCL Subject: CCL: nanocluster Message-Id: <-39052-090409165625-9022-JuTdBQlAwEamcQk8duHl8A|-|server.ccl.net> X-Original-From: Duy Le Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 9 Apr 2009 16:55:50 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle[*]gmail.com] Hi, Every elements can be used to model and study its cluster structure, stability... or what ever property you need. Good luck. On Thu, Apr 9, 2009 at 10:31 AM, neeraj misra neerajmisra[]hotmail.com wrote: > > Sent to CCL by: "neeraj =A0misra" [neerajmisra^-^hotmail.com] > I shall be extremely thankful to anyone who suggests me any series of ele= ments or system whose cluster can be modelled and studied for its structure= ,stability and energetics. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Men don't need hands to do things! From owner-chemistry@ccl.net Thu Apr 9 18:25:00 2009 From: "Marius Retegan marius.s.retegan]-[gmail.com" To: CCL Subject: CCL:G: Fixing coordinate system in Gaussian Message-Id: <-39053-090409182322-13852-Zay2eQ5fXC72GWGpVUTeMA[a]server.ccl.net> X-Original-From: Marius Retegan Content-Type: multipart/alternative; boundary=001636d348a02c924e046726b1aa Date: Fri, 10 Apr 2009 00:23:05 +0200 MIME-Version: 1.0 Sent to CCL by: Marius Retegan [marius.s.retegan*o*gmail.com] --001636d348a02c924e046726b1aa Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Maybe the nosymm keword in the input section can do the trick. Marius On Thu, Apr 9, 2009 at 10:53 PM, Duy Le ttduyle ~ gmail.com < owner-chemistry^ccl.net> wrote: > > Sent to CCL by: Duy Le [ttduyle**gmail.com] > It is better this way so that Gaussian can improve speed of > calculation due to some needed geometry operations. Writing a tiny > code to translate it (if necessary) will be the cheaper. :-) > > On Thu, Apr 9, 2009 at 11:53 AM, Mike Clark mike.clark28#%#yahoo.co.uk > wrote: > > > > Sent to CCL by: "Mike Clark" [mike.clark28{}yahoo.co.uk] > > Hi all > > > > I am trying to do a single point calculation in Gaussian, the input is in > cartesian coordinates, but the definition for the coordinate system are > translated/rotated in the results file, is there anyway to force gaussian to > use the fix input coordinates, while its possible to convert the results to > the origin coordinates its just seems alot of unnecessary work, there must > be an easier way to do this. > > > > Best > > > > Mike Clark> > > > > > > > > -- > Men don't need hands to do things! > > > > - This is automatically added to each message by the mailing script -> > > --001636d348a02c924e046726b1aa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Maybe the nosymm keword in the input section can do the trick.

Mariu= s

On Thu, Apr 9, 2009 at 10:53 PM, Duy Le= ttduyle ~ gmail.com <= ;owner-chemistry^ccl.net>= wrote:

Sent to CCL by: Duy Le [ttduyle**gmail.com]
It is better this way so that Gaussian can improve speed of
calculation due to some needed geometry operations. Writing a tiny
code to translate it (if necessary) will be the cheaper. :-)

On Thu, Apr 9, 2009 at 11:53 AM, Mike Clark mike.clark28#%#yahoo.co.uk
<owner-chemistry^-^ccl.net<= /a>> wrote:
>
> Sent to CCL by: "Mike =A0Clark" [mike.clark28{}yahoo.co.uk]
> Hi all
>
> I am trying to do a single point calculation in Gaussian, the input is= in cartesian coordinates, but the definition for the coordinate system are= translated/rotated in the results file, is there anyway to force gaussian = to use the fix input coordinates, while its possible to convert the results= to the origin coordinates its just seems alot of unnecessary work, there m= ust be an easier way to do this.
>
> Best
>
> Mike Clark
>
>
>
> -=3D This is automatically added to each message by the mailing = script =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= ge> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 = =A0 =A0http:/= /www.ccl.net/spammers.txt>
>
>



--
Men don't need hands to do things!

--001636d348a02c924e046726b1aa-- From owner-chemistry@ccl.net Thu Apr 9 23:39:01 2009 From: "Jeff Klenc jklenc1]*[student.gsu.edu" To: CCL Subject: CCL: trouble creating tables in SYBYL SPL Message-Id: <-39054-090409213849-12086-s3MeTf3BJvDvEX8NgB5rVw,,server.ccl.net> X-Original-From: "Jeff Klenc" Date: Thu, 9 Apr 2009 21:38:46 -0400 Sent to CCL by: "Jeff Klenc" [jklenc1!^!student.gsu.edu] I'm aiming for a script that simply creates a database backed table in SYBYL but cannot seem to get it quite right. The script always gets hung when entering the table name or database to back from. The pertinent lines are below. Wondering if anyone had clues? ############# setvar db %prompt(filename "database containing compounds:") setvar db_list %database(list *) setvar n %count($db_list) setvar table_name %cat($db_list "_1) table create $db database $db $db M1 || ############# This seems a very simple task, but I'm a beginner. Any help is greatly appreciated Thanks, Jeff