From owner-chemistry@ccl.net Thu May 29 05:22:00 2008 From: "Uwe Huniar uwe.huniar*cosmologic.de" To: CCL Subject: CCL: Turbomole: constrained optimization stops at the 3rd step Message-Id: <-37057-080529051737-12916-Y+dZXlzaw/ecsJLLHJWbQQ===server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 29 May 2008 11:18:11 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar[]cosmologic.de] Hello, I do not remember that in detail any more, but I think Turbomole 5.7.1 had a problem with fixed coordinates using symmetry during the optimization in some cases. This has been fixed in 5.8 or 5.9. You might consider upgrading Turbomole to the latest version - if you send your input to the Turbomole support, it can be easily tested with latest relax version to see if it works or not (and I guess it will...). Regards, Uwe > I am looking for a transition state in the reaction between H2 molecule and a > complex of N2 molecule coordinated to a 4-atom transition metal cluster > supported at MgO(100) surface. I use the constrained optimization with 1 > internal coordinate fixed (distance between the transition metal atom and > hydrogen atom). However, for two different values of the fixed internal > coordinate I got the same problem: optimization stopped at the 3rd step at > the relax stage, producing the following end of a job.3 file: > > MODTRACE: no modules on stack > > GETOLD : gradient mismatch ! relax ended abnormally relax step ended > abnormally next step = relax RELAX termination criterium:=0 > > Could anybody please advise me what the problem here could be? I use the > Turbomole version 5.7.1. From owner-chemistry@ccl.net Thu May 29 07:15:01 2008 From: "Ali S alsa38\a/gmail.com" To: CCL Subject: CCL: Maximum Force Message-Id: <-37058-080528064320-14810-VQuVDNvbAkjrLb6/gfNpGA##server.ccl.net> X-Original-From: "Ali S" Content-Type: multipart/alternative; boundary="----=_Part_7398_687016.1211967616903" Date: Wed, 28 May 2008 13:10:16 +0330 MIME-Version: 1.0 Sent to CCL by: "Ali S" [alsa38*|*gmail.com] ------=_Part_7398_687016.1211967616903 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Ol Ga Thank you very much. Your advise was very helpful. Sincerely yours. Ali S On 5/22/08, Ol Ga eurisco1!^!pochta.ru wrote: > > > Sent to CCL by: "Ol Ga" [eurisco1[*]pochta.ru] > Dear Ali! > You have forgoten polarization p-functions to > describe H-bonds. Try LanL2DZ/D95(d,p) with method B3lyp or > LanL2DZ/6-31G** with method B3lyp. > It is neccesary to add Diffuse basis functions > > Ol Ga > > > > > > Dear all > > > > I hope you are fine. I have a problem in the optimization process. > > in fact in this process the maximum force is high and appeare as ***** in > the threshold value. i am working in dimer of complex of transition metal > with organic ligands which intreact with each other with strong hydrogen > bonding. > > I use lanl2dz & 6-31G basis sets with B3lyp method. > > > > Can you help me about this? > > > > thanks. > > > > Ali S> > > ------=_Part_7398_687016.1211967616903 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear Ol Ga
 
Thank you very much.
Your advise was very helpful.
 
Sincerely yours.
Ali S

 
On 5/22/08, Ol Ga eurisco1!^!pochta.ru <owner-chemistry-,-ccl.net> wrote:

Sent to CCL by: "Ol  Ga" [eurisco1[*]pochta.ru]
Dear Ali!
You have forgoten polarization p-functions to
describe H-bonds.  Try LanL2DZ/D95(d,p) with method B3lyp  or
LanL2DZ/6-31G** with method B3lyp.
  It is neccesary to add Diffuse basis functions

Ol Ga




> Dear all
>
> I hope you are fine. I have a problem in the optimization process.
> in fact in this process the maximum force is high and appeare as ***** in the threshold value. i am working in dimer of complex of transition metal with organic ligands which intreact with each other with strong hydrogen bonding.
> I use lanl2dz & 6-31G basis sets with B3lyp method.
>
> Can you help me about this?
>
> thanks.
>
> Ali S



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------=_Part_7398_687016.1211967616903-- From owner-chemistry@ccl.net Thu May 29 10:19:00 2008 From: "Jesus Seco (Farmacia) jseco ~~ mmb.pcb.ub.es" To: CCL Subject: CCL: Which Drug Design s/w to be Bought for Academic Research Message-Id: <-37059-080528133142-28077-6R59eHo5yTuc1cnzptpaTg{:}server.ccl.net> X-Original-From: "Jesus Seco (Farmacia)" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 28 May 2008 18:33:56 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Jesus Seco (Farmacia)" [jseco(-)mmb.pcb.ub.es] I suggest you to have a quick look at MOE website, because it offers almost that all you need. The problem, is non-academic software, but you have a wide range of functionalities. The website is the following : http://www.chemcomp.com/ I hope it will be useful for your purpose On Tue, 27 May 2008, gajuguard-ccl{:}yahoo.co.in wrote: > Respected Sir / Madam, >   > Our's is the Pharmacy Dept in the SGSITS, an Autonomous Institute in MP, INDIA. > We are in process to buy a drug design software for the purpose of doing basic research in drug design (non-profit purpose) for > - QSAR > - Docking > - Pharmacophore modeling > - prediction of ADME parameters > - & other accessories >   > So, we are in search of a drug design software to be bought in thedept't which is economic, with out time limitation, with neccessary accurary & predictability in results for academic research. >   > Kindly have some suggestions. >   > Thanking you. >   > Sincerely, > Gajanan Wanare, > Dept't of Pharmacy, > Shri G S Institute of Technology & Science (SGSITS), > Indore- (MP) INDIA. > www.sgsits.ac.in > gajuguard-ccl(_)yahoo.co.in Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ From owner-chemistry@ccl.net Thu May 29 12:06:00 2008 From: "Prema Mallipeddi plmallip=mail.uh.edu" To: CCL Subject: CCL: Modelling a pentamer, problem with retaining position of chains Message-Id: <-37060-080529091718-6651-XQgbHFkI4CAcusvWbDmiOg%x%server.ccl.net> X-Original-From: "Prema Mallipeddi" Date: Thu, 29 May 2008 09:17:14 -0400 Sent to CCL by: "Prema Mallipeddi" [plmallip*o*mail.uh.edu] Modelling a pentamer, problem with retaining position of chains - overlapping or orientation problem. Is it possible? Dear colleagues, I have a protein with 5 chains. I initially modelled all the 5 chains using a template, using MODELLER 8v1. But, some of the chains have missing residues at a particular region. This region is missing even in the corresponding chains of reference structure. So, to particularly model that region, I followed steps. 1. Model pentamer at one instance using another pentamer as template. 2. For the missing residues, for e.g. model C chain (with missing residues) of the protein, using E chain as the template. 3. Overlay Chain C from step 1 and step 2. Save pdbs in this orientation. Copy only that stretch of residues of Chain C to the Chain C obtained from step 1. 4. Does the same thing for Chain B as well. 5. But, when I assemble the protein again, chains B and C at overlapping with chain E. The pentamer thus has 3 chains at one place. I tried using VMD "RMSD tool" and also InsightII. But, I couldn't save chains B and C from step 3, in the same orientation, as they were in step 1. Is there anyway, I can place the chains again in the same pentameric way? Do I end up in a good model this way? Thanks & regards, Prema. From owner-chemistry@ccl.net Thu May 29 13:16:00 2008 From: "Simon Cross simon * moldiscovery.com" To: CCL Subject: CCL: Which Drug Design s/w to be Bought for Academic Research Message-Id: <-37061-080529122520-24058-VuxkDEQQpfR/RU88oDVRWQ*server.ccl.net> X-Original-From: Simon Cross Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 29 May 2008 16:28:42 +0100 MIME-Version: 1.0 Sent to CCL by: Simon Cross [simon%moldiscovery.com] Hi Gajanan, there are many many tools out there that cover all of the areas you mention, including 'free to academic/non-profit' software, that you can probably find out about by searching the CCL archives. It is probably worth considering: 1. Do you want commercial quality code? With support, training etc? 2. Do you want integration, all in one package? 3. Do you prefer to have the 'best' software for each application area, even though you may need to transfer data from one to another? 4. How much money, if any, do you want to spend? 5. The 'accessories' you describe may be key to your decision; think whether you need 2D-3D conversion, minimizers, dynamics, 3D sketchers, file format conversion, chemical library enumeration, 2D fingerprint searching, diversity analysis, protein structure preparation/modelling etc. Some packages will have them by default, others won't. The major commercial vendors that offer fully integrated packages are Tripos (www.tripos.com), Accelrys (www.accelrys.com), CCG (www.chemcomp.com), Schrodinger (www.schrodinger.com), in no particular order. Others include OpenEye (www.eyesopen.com) and ourselves (Molecular Discovery - www.moldiscovery.com), and there are others that I apologise in advance for neglecting to mention. Each has strengths and weaknesses. Most have 'special discounts' for academics, certainly we only charge a nominal fee. Scientific performance will also depend on the targets you are working on. If I were you, and I had some time, I would look into each, and perhaps contact them to evaluate the software in advance of any purchase to ensure it works for what you want to do. Kind Regards, Simon -- Simon Cross Snr Scientist & Product Manager Molecular Discovery Ltd Tel 07980 572278 www.moldiscovery.com gajuguard-ccl{:}yahoo.co.in wrote: > Respected Sir / Madam, > > Our's is the Pharmacy Dept in the SGSITS, an Autonomous Institute in > MP, INDIA. > We are in process to buy a drug design software for the purpose of > doing basic research in drug design (non-profit purpose) for > - QSAR > - Docking > - Pharmacophore modeling > - prediction of ADME parameters > - & other accessories > > So, we are in search of a drug design software to be bought in > thedept't which is economic, with out time limitation, with neccessary > accurary & predictability in results for academic research. > > Kindly have some suggestions. > > Thanking you. > > Sincerely, > Gajanan Wanare, > Dept't of Pharmacy, > Shri G S Institute of Technology & Science (SGSITS), > Indore- (MP) INDIA. > www.sgsits.ac.in > gajuguard-ccl(_)yahoo.co.in > > > ------------------------------------------------------------------------ > Best Jokes, Best Friends, Best Food. Get all this and more on Best of > Yahoo! Groups. > From owner-chemistry@ccl.net Thu May 29 14:40:00 2008 From: "Ben Webb ben|a|salilab.org" To: CCL Subject: CCL: Modelling a pentamer, problem with retaining position of chains Message-Id: <-37062-080529140608-5034-lPUcNGyI31taDpz109UldA(!)server.ccl.net> X-Original-From: Ben Webb Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 29 May 2008 09:40:47 -0700 MIME-Version: 1.0 Sent to CCL by: Ben Webb [ben a salilab.org] Prema Mallipeddi plmallip=mail.uh.edu wrote: > Modelling a pentamer, problem with retaining position of chains - overlapping or orientation problem. Is it possible? > > Dear colleagues, I have a protein with 5 chains. I initially modelled all the 5 chains using a template, using MODELLER 8v1. But, some of the chains have missing residues at a particular region. This region is missing even in the corresponding chains of reference structure. So, to particularly model that region, I followed steps. > > 1. Model pentamer at one instance using another pentamer as template. > 2. For the missing residues, for e.g. model C chain (with missing residues) of the protein, using E chain as the template. > 3. Overlay Chain C from step 1 and step 2. Save pdbs in this orientation. Copy only that stretch of residues of Chain C to the Chain C obtained from step 1. > 4. Does the same thing for Chain B as well. > 5. But, when I assemble the protein again, chains B and C at overlapping with chain E. The pentamer thus has 3 chains at one place. Why don't you just combine steps 1 and 2 into a single step? Modeller can build models using multiple templates, and will sort out the orientation for you. So your alignment would look something like: AAAA/BBBB/CC-C/DDDD/EEEE (template 1) ----/----/EEEE/----/---- (template 2) aaaa/bbbb/cccc/dddd/eeee (target sequence) Here 'template 2' is just another copy of the first pentameric template, using only the E chain, to fill in the missing residues in the C chain. Ben -- ben^salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle