From owner-chemistry@ccl.net Sat Feb 20 03:20:01 2010 From: "Andrew Voronkov drugdesign:yandex.ru" To: CCL Subject: CCL: can you recommend software to compare chemical databases and exclude duplicates pls Message-Id: <-41287-100219124556-24607-3pq3f2Yh7sdBPp9bfPdpuw]=[server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 19 Feb 2010 20:45:41 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign%yandex.ru] Dear CCL users, can you please recommend me academics free software or scripts (or software with good evaluation period) for comparison of databases. For example I want to download two publically available databases and unite them excluding duplicates into a separate database. So in this case I ll get one united database and one database where duplicate compounds will be (but not duplicated). Can you please suggest such software? Sincerely yours, Andrew From owner-chemistry@ccl.net Sat Feb 20 03:55:01 2010 From: "Andreas Klamt klamt]~[cosmologic.de" To: CCL Subject: CCL: Estimation of viscosity from molecular weight (Erratum) Message-Id: <-41288-100220020223-2228-pGttBfP1mNeDzMIkkqdtsg(~)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 20 Feb 2010 08:01:57 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt|-|cosmologic.de] Hi all, sorry, I have to correct my prevous message: Obviously the relation between entropy and viscosity is the other way round: If the liquid has a high entropy, it has a lot of contact partner changes and hence a low resistance to shear, i.e. a low viscosity. Andreas Andreas Klamt klamt,cosmologic.de schrieb: > > Sent to CCL by: Andreas Klamt [klamt[#]cosmologic.de] > Hi Alex, > > an estimation of viscosity just from molecular weight is obviously > nonsense. No question, there is a considerable influence of the > molecular size (for which the weight may be a descriptor, but probably > volume or surface area are the better descriptors), but in addition > viscosity has a lot to do with the interactions of the molecules. > > Our COSMOtherm software includes a model for viscosity, based on the > molecular surface area and on the entropy of the liquid. The entropy is > calculated by COSMO-RS, and it is a measure of the degree of partner > changes. If each surface segment has a lot if different > thermodynamically available choices for the interaction partner, then > the entropy is high, and the liquid has a high viscosity, and vice > versa. Obviously this is not absolutely rigorous, but at least quite > plausible and it works quite well. > > Best regards > > Andreas > > Alex Naden anaden**fsmail.net schrieb: >> Sent to CCL by: "Alex Naden" [anaden|*|fsmail.net] >> Hi, >> >> I am trying to find a way of estimating viscosity from molecular >> weight. I have found some information on Joback/Reid method but I am >> not sure if there is a software implementing this method or any >> alternative way to estimate the viscosity? I would be grateful if >> someone could help with this. >> >> Thank you, >> >> Alex> >> >> >> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt : cosmologic.de web www.cosmologic.de HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Sat Feb 20 06:05:01 2010 From: "sina rastegar sina_rastegar1979^-^yahoo.com" To: CCL Subject: CCL: optimaization problem Message-Id: <-41289-100220060312-7976-rOxrzsTLA1ASJJBsICDXwA---server.ccl.net> X-Original-From: "sina rastegar" Date: Sat, 20 Feb 2010 06:03:08 -0500 Sent to CCL by: "sina rastegar" [sina_rastegar1979#%#yahoo.com] I am trying to optimize a cluster of heterofullerene(c48 b12)which is dopped with calcium.after I want to study the absorption of hydrogen H2 on this compound.I have used oniom but unfortunately an error occured during the optimization. Anihilation of the first spin contaminant is the reason of this error. I am really confused and I do not know what to do. From owner-chemistry@ccl.net Sat Feb 20 10:36:01 2010 From: "S. Bill s_bill36**yahoo.co.uk" To: CCL Subject: CCL: PM3 reparameterization software Message-Id: <-41290-100219230730-30723-rqcJMfMwtDZzFoprJLxzbg ~ server.ccl.net> X-Original-From: "S. Bill" Date: Fri, 19 Feb 2010 23:07:26 -0500 Sent to CCL by: "S. Bill" [s_bill36,,yahoo.co.uk] Dear CCL I am working on reparameterization of semi-empirical PM3 parameters of certain ions. I was wondering if anybody knows any free semi-empirical PM3 parameterization software (included Generic Algorithm). Thanks in advance S. Bill From owner-chemistry@ccl.net Sat Feb 20 11:11:01 2010 From: "Wolf-D. Ihlenfeldt wdi**xemistry.com" To: CCL Subject: CCL: AW: can you recommend software to compare chemical databases and exclude duplicates pls Message-Id: <-41291-100220080542-27446-er1nFeQgxQ3KBxsq40Lppg#server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 20 Feb 2010 14:05:58 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi]![xemistry.com] You can do that easily with the academic version of the CACTVS toolkit (www.xemistry.com/academic).=20 The software includes functions to compute a broad collection of = hashcodes of various types (i.e. with/without stereochemistry/isotopes/etc.), = which are so reliable that there are no known collisions.=20 Here is a minimal sample script (9 actual code lines, excluding comments = and closing brace lines): ---snip---- # open file set as a single virtual file set fh [molfile lopen $args r hydrogens add] # loop over all structures molfile loop $fh eh { # compute gen2 hashcode with stereo and isotopes, and remember record numbers lappend hashes([ens get $eh E_HASHISY]) [expr [molfile get $fh vrecord]-1] } # open output files set fhout1 [molfile open singletons.sdf w] set fhout2 [molfile open dups.sdf w] # write out a record into the proper result file for each first instance = of a hashcode foreach hash [array names hashes] { # position virtual input file to record of first hash code instance molfile set $fh vrecord [lindex $hashes($hash) 0] # write a byte-exact copy to the proper output channel molfile copy $fh [expr {[llength $hashes($hash)]=3D=3D1 ? $fhout1 : $fhout2}] } molfile close all ---snip---- Run with the generic script interpreter=20 csts -f script.tcl datafile1 datafile2... > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry+wdi=3D=3Dxemistry.com() ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com() ccl.net] Im Auftrag von Andrew = Voronkov > drugdesign:yandex.ru > Gesendet: Freitag, 19. Februar 2010 18:46 > An: Ihlenfeldt, Wolf D > Betreff: CCL: can you recommend software to compare chemical databases > and exclude duplicates pls >=20 >=20 > Sent to CCL by: Andrew Voronkov [drugdesign%yandex.ru] > Dear CCL users, > can you please recommend me academics free software or scripts (or > software with good evaluation period) for comparison of databases. For > example I want to download two publically available databases and = unite > them excluding duplicates into a separate database. So in this case I > ll get one united database and one database where duplicate = compounds > will be (but not duplicated). Can you please suggest such software? >=20 > Sincerely yours, > Andrew >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20 From owner-chemistry@ccl.net Sat Feb 20 19:13:00 2010 From: "CompChem Group CompChemGroup1_+_gmail.com" To: CCL Subject: CCL: Long time Geometry optimization Message-Id: <-41292-100220172505-9496-zjW5eGd/7SBBmEIsJtBDqQ,+,server.ccl.net> X-Original-From: "CompChem Group" Date: Sat, 20 Feb 2010 17:25:02 -0500 Sent to CCL by: "CompChem Group" [CompChemGroup1-.-gmail.com] Dear All, Currently, I preform geometry optimization of Dinuclear metal complex (two Cu atoms + 100 of H, C, N and O atoms)in order to calculate thermodynamic parameters. I use B3LYP/mixed basis set; 6-311g(d,p)for H, C, N and O atoms and LANL2DZ for Cu. I use 8 cores for this job. This job consumed long time; about 20 days and not finished so far. I have two questions: 1- Is normal for such job to take this long time? 2- Is this basis set is good to calculate the thermodynamic parameters? 3- Is there a model chemistry or a method work well but with little time? By the way the H-atoms are not important, so I can use 6-311g without polarization functions. Your suggestion would be appreciated Thanks in advance, C.C.G From owner-chemistry@ccl.net Sat Feb 20 19:48:00 2010 From: "Sayed Mes Elsayed.elmes(_)yahoo.com" To: CCL Subject: CCL: Geometry optimization and Single point Scaling Message-Id: <-41293-100220175641-10939-R8tSXgpo7fOe8TzbI3M3xw_._server.ccl.net> X-Original-From: "Sayed Mes" Date: Sat, 20 Feb 2010 17:56:38 -0500 Sent to CCL by: "Sayed Mes" [Elsayed.elmes]^[yahoo.com] Dear Subscribers, I preformed scaling for "Geometry optimization (only 4 steps)" and "Single point Scaling" for first row transition metal complex with 1,2,4 and 8 cores on MPI cluster. DFT method is used for this purpose. I found that there is no difference among them; i.e. the time consuming with 1 core is nearly the same like 2 or 4 or 8 cores. Anybody know why there is no difference in consuming time among them? Thanks, Sayed From owner-chemistry@ccl.net Sat Feb 20 20:25:01 2010 From: "Vincent Leroux vincent.leroux*_*loria.fr" To: CCL Subject: CCL: can you recommend software to compare chemical databases and exclude duplicates pls Message-Id: <-41294-100220082813-29185-vLTdYrR+gURSBNfHUFnERg|server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 20 Feb 2010 14:27:38 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux+*+loria.fr] Hi Andrew, There is ScreeningAssistant for such a task, and much more. http://hal.archives-ouvertes.fr/docs/00/07/97/12/PDF/monge_Molecular_Diversity_revised_2.pdf http://dx.doi.org/10.1007/s11030-006-9033-5 http://dx.doi.org/10.2174/157340908785747410 SA is really boxing in the heavyweight category of chemoinformatics tools so you might prefer to process data by yourself. My suggestions : - first "clean up" db1.sdf and db2.sdf: remove salts, hydrogens etc. everything in the structure that might differ artificially from one supplier to the other. (Open)Babel should do a good job here. - name all molecules in db1.sdf and db2.sdf using scripts. The name must be on the 1st line in each molecule record and should not contain spaces. You want a combination of the supplier name and the molecule supplier's unique ID (already in place if you are lucky, else found in some MDL tag). Make sure the name does not contain spaces, and that is is put in the correct position (1st line). - use the InChI software for generating db1.inchi and db2.inchi, and make sure you get text files with 1 line per molecule formatted like: - If the molecules are named Supplier1/ and Supplier2/ , then use the following commands (have not tested them, but should work) cat db[12].inchi | sort -k2 | uniq -s 1 - | grep '^Supplier1/' > db1_unique.inchi cat db[12].inchi | sort -k2 | uniq -s 1 - | grep '^Supplier2/' > db2_unique.inchi cat db[12].inchi | sort -k2 | uniq -d -s 1 - | awk '{l=$1; getline; print l"_aka_"$0}' > db12_common.inchi This will generate db1_unique.inchi, db2_unique.inchi and db12_common.inchi - self-explanatory. - use OpenBabel (or equivalent software) for converting your InChI files to SDF format/2D representation, then Corina (or equivalent) if you want 3D coordinates, e.g. for docking. Regards, VL Le 19/02/10 18:45, Andrew Voronkov drugdesign:yandex.ru a écrit : > > Sent to CCL by: Andrew Voronkov [drugdesign%yandex.ru] > Dear CCL users, > can you please recommend me academics free software or scripts (or software with good evaluation period) for comparison of databases. For example I want to download two publically available databases and unite them excluding duplicates into a separate database. So in this case I ll get one united database and one database where duplicate compounds will be (but not duplicated). Can you please suggest such software? > > Sincerely yours, > Andrew > > From owner-chemistry@ccl.net Sat Feb 20 23:14:00 2010 From: "David Mannock dmannock===ualberta.ca" To: CCL Subject: CCL: Estimation of viscosity from molecular weight (Erratum) Message-Id: <-41295-100220164840-7502-0vQ6yv7Ss0c1s1uTl02vTQ_-_server.ccl.net> X-Original-From: David Mannock Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 20 Feb 2010 13:56:43 -0700 MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock]^[ualberta.ca] Ahh! Yes, but in a parallel universe somewhere far, far away......... Sorry Andreas, I couldn't resist! Dave On 2/20/2010 12:01 AM, Andreas Klamt klamt]~[cosmologic.de wrote: > > Sent to CCL by: Andreas Klamt [klamt|-|cosmologic.de] > Hi all, > > sorry, I have to correct my prevous message: Obviously the relation > between entropy and viscosity is the other way round: > If the liquid has a high entropy, it has a lot of contact partner > changes and hence a low resistance to shear, i.e. a low viscosity. > > Andreas > > Andreas Klamt klamt,cosmologic.de schrieb: >> >> Sent to CCL by: Andreas Klamt [klamt[#]cosmologic.de] >> Hi Alex, >> >> an estimation of viscosity just from molecular weight is obviously >> nonsense. No question, there is a considerable influence of the >> molecular size (for which the weight may be a descriptor, but probably >> volume or surface area are the better descriptors), but in addition >> viscosity has a lot to do with the interactions of the molecules. >> >> Our COSMOtherm software includes a model for viscosity, based on the >> molecular surface area and on the entropy of the liquid. The entropy is >> calculated by COSMO-RS, and it is a measure of the degree of partner >> changes. If each surface segment has a lot if different >> thermodynamically available choices for the interaction partner, then >> the entropy is high, and the liquid has a high viscosity, and vice >> versa. Obviously this is not absolutely rigorous, but at least quite >> plausible and it works quite well. >> >> Best regards >> >> Andreas >> >> Alex Naden anaden**fsmail.net schrieb: >>> Sent to CCL by: "Alex Naden" [anaden|*|fsmail.net] >>> Hi, >>> >>> I am trying to find a way of estimating viscosity from molecular >>> weight. I have found some information on Joback/Reid method but I am >>> not sure if there is a software implementing this method or any >>> alternative way to estimate the viscosity? I would be grateful if >>> someone could help with this. >>> >>> Thank you, >>> >>> Alex> >>> >>> >> >> > >