From owner-chemistry@ccl.net Mon Jun 8 02:26:01 2009 From: "Arvydas Tamulis tamulis*o*itpa.lt" To: CCL Subject: CCL: Problems with ORCA Message-Id: <-39464-090608022243-8517-Go2tmmv4z0ex0XKpXuupvA]*[server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 8 Jun 2009 08:43:56 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis]*[itpa.lt] Dear Colleagues, When trying to run MPI Orca SCF calculation on same multi-core server, SCF ends up with error message that it can't access .GBW file. Question is if it's possible to use same directory as scratch directory for parallel Orca calculation, when all parallel SCF calculation processes access same data? This above problem is on Intel Xeon 8 cores server and using the appropriate version of ORCA. Sometimes on AMD64 8 cores server with AMD ORCA version we obtaining result which is corrupted. Maybe origin of this corruption is coming from the above described problem? ------------------------------------------------------------------- CD SPECTRUM ------------------------------------------------------------------- State Energy Wavelength R MX MY MZ (cm-1) (nm) (1e40*sgs) (au) (au) (au) ------------------------------------------------------------------- 1 -0.0 -90066368839371800576.0 -0.00000 -0.00000 -0.00000 0.00000 2 0.0 443697243141010948096.0 0.00000 0.00000 -0.00000 -0.00000 3 0.0 22813909805381799936.0 -0.00000 -0.00000 0.00000 0.00000 4 0.0 15867989671719761920.0 0.00000 0.00000 0.00000 -0.00000 5 0.0 13284546321436213248.0 0.00000 0.00000 -0.00000 -0.00000 6 0.0 5933787844289631232.0 -0.00000 0.00000 -0.00000 0.00000 7 0.0 2823038586214064128.0 0.00000 -0.00000 -0.00000 -0.00000 8 0.0 1755309658072443392.0 -0.00000 0.00000 -0.00000 -0.00000 9 0.0 1533138598263405568.0 -0.00000 -0.00000 0.00000 0.00000 10 0.0 1356227485917171456.0 -0.00000 -0.00000 0.00000 0.00000 11 18834.7 530.9 -8.72536 -0.00266 0.00458 0.08674 12 18997.0 526.4 -2.22650 0.03580 -0.00807 0.03564 13 19434.8 514.5 0.29907 0.08593 -0.01122 0.02892 14 20038.4 499.0 0.00000 0.00000 -0.00005 0.00010 15 20066.8 498.3 0.00000 -0.00000 -0.00003 0.00002 16 20294.2 492.8 0.00005 0.00001 -0.00016 0.00036 17 20648.0 484.3 -1.56080 0.00363 0.00168 -0.03702 18 23540.9 424.8 -4.02444 -0.02716 0.24427 0.11972 19 25766.8 388.1 64.76382 0.14545 0.04547 0.74386 20 26321.8 379.9 0.73897 0.03049 -0.00199 -0.01965 21 28066.8 356.3 -55.09782 -0.27694 0.02802 0.24577 22 30719.1 325.5 71.12387 0.16317 -0.15543 0.17809 23 33748.6 296.3 0.01819 -0.00290 0.00340 0.00325 24 34480.6 290.0 0.07716 0.00565 -0.01883 -0.00690 25 35288.4 283.4 0.00053 0.00250 0.00002 -0.00179 With best regards, Arvydas http://www.itpa.lt/~tamulis/ From owner-chemistry@ccl.net Mon Jun 8 03:00:00 2009 From: "Andreas Klamt klamt||cosmologic.de" To: CCL Subject: CCL: PH-dependent ab-initio calculations Message-Id: <-39465-090608014819-6154-OIx7Prv3tRih/ECs50966w~~server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 08 Jun 2009 07:47:27 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt. a .cosmologic.de] Dear Yutao Yue, just upfront: COSMOtherm is the name of our COSMO-RS program. The theory = itslef has the name COSMO-RS. Just to avoid confusion. Let me try to answer your further questions: > Is it true that for those molecules without any chance of grabbing and = > releasing H+ (protonation state) or OH- (not sure how to name that),=20 > the pH of solvent has no influence on the properties of the molecule?=20 > Or maybe some but limited influence? If otherwise what kind of=20 > influence would it be? (I assume that solvent are always neutral while = > separate charges H3O+ and OH- have very low concentration comparing to = > the solvent itself) Yes, that is true. > On the other hand, for molecules like individual amino acids or=20 > proteins, other than adding/subtracting H+/OH- to the chemical=20 > structure of the molecules (and the subsequent changes in structures=20 > and other properties), are there any other significant influence of pH = > on the molecules? Even for amino acids and proteins: The pH influences the balance of the=20 different protonation forms. This then has an influence on the structure = and properties. Andreas > > Sorry for bringing up more questions and I really appreciate your time = > and help. > > Regards, > Yutao Yue > > On Fri, Jun 5, 2009 at 2:19 AM, Andreas Klamt klamt++cosmologic.de=20 > > wrote: > > > Sent to CCL by: Andreas Klamt [klamt(a)cosmologic.de > ] > Dear Yutao, > > pH-dependent ab-initio calculations in general are impossible. The > pH of > the solvent does change the equilibrium between protonated and > deprotonated species, but you will always have to decide which spec= ies > you want to consider in your ab-initio calculation. (in the > following I > assume that you mean generally QM methods, including DFT, when you = say > ab-initio). Beyond the H3O+ and OH- concentrations, which anyway ar= e > very small, the pH does not change the solvent properties > significantly. > I.e. what you need to do is to calculate the protonated and > deprotonated > species in your solvent (usually water) using a good solvation mode= l, > calculate the pKa from the free energy difference of both solvated > species, and then calculate the population of the species at a > given pH. > > Our COSMOtherm program in combination with a QM propgram being able= to > write the required DFT/COSMO files, e.g. TURBOMOLE, does provide th= e > infrastructure to do so, not only in water but in any solvent. > > Andreas > > Yutao Yue Yutao.Yue*_*gmail.com schrieb: > > Sent to CCL by: "Yutao Yue" [Yutao.Yue^_^gmail.com > ] > Hello dear friends, does anybody know how to do an ab-initio > calculation of a molecular system under a certain PH value? > Has there been much development on PH-dependent ab-initio > methods? Maybe some PH-dependent empirical methods? Thanks for > any information. > > Regards, > Yutao Yue > > > > --=20 > PD. Dr. Andreas Klamt > CEO / Geschaeftsf=FChrer > 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 > > > > > - This is automatically added to each message by the mailing script= - > > > > E-mail to subscribers: CHEMISTRY(!)ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/=> > > --=20 PD. Dr. Andreas Klamt CEO / Geschaeftsf=FChrer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt a 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 Mon Jun 8 05:46:00 2009 From: "Vincent.Leroux-$-loria.fr" To: CCL Subject: CCL: Docking-scoring functions Message-Id: <-39466-090608054246-16598-EtOfFtEPOf9Aegy1B/lwfw%a%server.ccl.net> X-Original-From: Vincent.Leroux^_^loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 08 Jun 2009 11:42:36 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux**loria.fr Hi, Scoring functions used by most docking programs are notoriously =20 inaccurate, so the "best" virtual screening approach for ranking a set =20 of ligands might be not to use a scoring function in the first place. As for docking programs, the quality of search algorithm is in my =20 opinion more important than the accuracy of the scoring function. If =20 you have a good scoring function but a lousy search algorithm, you =20 might end up with a well-characterized but not very useful local =20 minimum. In the reverse situation, you have a greater chance of ending =20 up closer, hopefully close enough, to the global minimum. To my knowledge, most docking programs belong to the second category. =20 They can do moderately well in building 3D structures of =20 protein-ligand complexes with acceptable RMSD deviation compared to =20 reference X-ray structures, but are often weak when it comes to =20 quantifying the modeled interaction. You should not expect good =20 correlations between IC50 and scoring values after performing a simple =20 docking calculation. If you want the best simplicity vs. efficiency =20 ratio, you should definitely favor the ligand-based approaches to =20 virtual screening... A much more relevant structure-based strategy might be to use first =20 docking programs that are best for conformational searching (e.g. =20 those based on genetic algorithms, ant colony optimization...), then, =20 in a second stage, throw away the scoring function and optimize a =20 limited set of proposed conformations (not just the docking program =20 best pick...) using better free energy of binding estimates. This is =20 similar to the integrated hierarchical narrowing protocol that Glide =20 uses (and that justifies its popularity amongst docking programs). =20 Sensible post-docking optimization can be based on MM/PBSA =20 minimization, this might be done with a bit of scripting and either a =20 molecular modeling package such as MOE or a specific tool like =20 OpenEye's Szybki. Good luck VL "Jesus Planesas planesaj~~hotmail.com" a =E9crit= =A0: > > Sent to CCL by: "Jesus Planesas" [planesaj*hotmail.com] > Dear all > > Before starting to dock a chemical library of potential ligands with =20 > MOE (chemcorp.com) I'm trying to evaluate the best docking/scoring =20 > MOE function using a set of ligands with known experimental IC_50. > > Anybody knows and article or a detailed job where I can see step by =20 > step an exemple of one evaluation like this? And if it's done with =20 > MOE it'll be fantastic > > Thanks > > Jesus > > > From owner-chemistry@ccl.net Mon Jun 8 07:08:01 2009 From: "James Justin Robinson james.robinson:prosonix.co.uk" To: CCL Subject: CCL: pH-dependent ab-initio calculations Message-Id: <-39467-090608054731-17548-wNGWW76mOpvkzWNGaAVLbA^_^server.ccl.net> X-Original-From: "James Justin Robinson" Date: Mon, 8 Jun 2009 05:47:27 -0400 Sent to CCL by: "James Justin Robinson" [james.robinson],[prosonix.co.uk] Hi Mahmoud, I heartily recommend you grab papers written by Liptak and Shields, there is debate over the entropy related to solvation of a proton in water. The solvation methods you use will affect the result. I have used Cosmo-RS as suggested by Andreas and you should ask more of him and the software developed that uses Cosmo-RS. james From owner-chemistry@ccl.net Mon Jun 8 07:44:00 2009 From: "Vincent.Leroux:loria.fr" To: CCL Subject: CCL: Do you have the experience about Stereo LCD monitor for molecular modeling? Message-Id: <-39468-090608060124-25755-0D3mwmnFJdmfLiQv9SJ1uw]-[server.ccl.net> X-Original-From: Vincent.Leroux*o*loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 08 Jun 2009 12:01:08 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux^_^loria.fr Hi, You cannot do it. Unfortunately, nVidia 3D vision glasses need drivers that are for the =20 moment only available for Windows. A good part of the molecular =20 modeling world cannot wait for using these glasses coupled with the =20 Samsung 120Hz LCD monitor on their Linux workstations. Be sure that when such Linux drivers will be made available the word =20 will spread quickly on this mailing list... VL "li_qiang_000739::wuxiapptec.com li_qiang_000739::wuxiapptec.com" =20 a =E9crit=A0: > > Sent to CCL by: "li_qiang_000739-x-wuxiapptec.com" =20 > [li_qiang_000739-x-wuxiapptec.com] > Dear all, > > Do you have the experience about Stereo LCD monitor for molecular modeling= ? > > We have a Samsung(r) SyncMaster 2233RZ 120 Hz LCD display, its =20 > resolution is 1680x1050. The signal input is DVI-DL. > > I try the LCD on one HP Xw6600 workstation with Quadro FX3700 =20 > graphics card. The operation system is CentOS 5.3, so I update the =20 > latest nVidia driver and set the xorg.conf with " Option =20 > "stereo" "3"". > > But I can get the hardware stereo in our modeling software. > > Who can tell me how to do it? Thank you for advance. > > Best regards, > > Li Qiang > > CADD Laboratory > WUXI AppTec Co., Ltd. > > E-mail: li_qiang_000739-.-wuxiapptec.com > > Address: No.1 Building, 288 Fute Zhong Road, WaiGaoQiao Free > Trade Zone, Shanghai, P.R.China > PostCode: 200131 > Tel: 86-21-50463316 > Fax: 86-21-50461000 > Web Site: www.wuxiapptec.com > > > From owner-chemistry@ccl.net Mon Jun 8 13:27:00 2009 From: "Shahar Keinan skeinan * gmail.com" To: CCL Subject: CCL: Question about GAMESS/TINKER - no link atoms Message-Id: <-39469-090607222001-26374-Zv9rANGh3iGFFqKRrWpOxQ|,|server.ccl.net> X-Original-From: "Shahar Keinan" Date: Sun, 7 Jun 2009 22:19:57 -0400 Sent to CCL by: "Shahar Keinan" [skeinan(0)gmail.com] Dear all, I am trying to do a QM/MM calculation with GAMESS/TINKER, however, I want to run the calculations without link atoms. Is this possible? The example files all have link atoms in them. Thank you, Dr. Shahar Keinan Duke University I am attaching an example of an input file that gets an error message (this is a water dimer, one water molecule QM, the other TIP3): ! An example file to perform ! QM/MM. ! water dimer, no link atoms. One water is TIP3, ! other water described with HF/STO-3G ! $CONTRL SCFTYP=RHF RUNTYP=optimize COORD=UNIQUE NZVAR=33 $END $BASIS GBASIS=sto NGAUSS=3 $END $ZMAT DLC=.T. AUTO=.T. $END $DATA Ab initio atoms in QM region C1 O 8.0 -0.032947 0.000000 0.005966 H 1.0 0.270601 0.000000 0.911928 H 1.0 0.792970 0.000000 -0.510216 $END $LINK IMOMM=.T. IQMATM(1)=1,2,3 $END $TINKEY parameters /home/skeinan/gamess_tinker/tinker/params/charmm $END $TINXYZ 6 water dimer 1 OT -0.032947 0.000000 0.005966 91 2 3 2 HT 0.270601 0.000000 0.911928 83 1 3 HT 0.792970 0.000000 -0.510216 83 1 4 HT 2.756636 0.756897 -1.740089 83 5 5 OT 2.373120 0.000000 -1.290448 91 4 6 6 HT 2.756636 -0.756897 -1.740089 83 5 $END From owner-chemistry@ccl.net Mon Jun 8 17:28:01 2009 From: "Adil R Zhugralin zhugrali*bc.edu" To: CCL Subject: CCL: Obtaining MP2 wavefunction Message-Id: <-39470-090608172709-27342-EYqXH5q29MT+r7VVkf+EGQ=-=server.ccl.net> X-Original-From: "Adil R Zhugralin" Date: Mon, 8 Jun 2009 17:27:05 -0400 Sent to CCL by: "Adil R Zhugralin" [zhugrali.(0).bc.edu] Dear CCL'ers, I am trying to get a MP2(full) densities for subsequent QTAIM analysis. My input is as follows: # mp2(full)/6-311+G(2d,2p) 6D 10F density=current output=wfn geom=connectivity scf(verytight,xqc) int=grid=ultrafine maxdisk=12800MW The name.wfn file reads at the end: END DATA THE HF ENERGY = -505.288094901958 THE VIRIAL(-V/T)= 2.00111969 The name.log file has the same E(RHF), and of course a lower EUMP2. The QTAIM analysis with the densities from name.wfn gives energies that sum up to the E(RHF). However, I need MP2 densities and MP2 energies. What am I doing wrong in trying to get the MP2 densities and energies? Thanks in advance. Adil Zhugralin ------------------------- Hoveyda Group, Department of Chemistry, Boston College ------------------------- From owner-chemistry@ccl.net Mon Jun 8 19:39:00 2009 From: "Warren DeLano warren**delsci.com" To: CCL Subject: CCL: Do you have the experience about Stereo LCD monitor for molecular modeling? Message-Id: <-39471-090608150132-9023-Dz/DSR6zbs1p1wuH+j+Abw a server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Mon, 8 Jun 2009 11:28:16 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren(a)delsci.com] Li, Stereo-3D-capable OpenGL drivers for this display have yet to be released by nVidia. However, they are expected soon... Cheers, Warren > -----Original Message----- > From: owner-chemistry+warren=3D=3Ddelsci.com:ccl.net [mailto:owner- > chemistry+warren=3D=3Ddelsci.com:ccl.net] On Behalf Of > li_qiang_000739::wuxiapptec.com li_qiang_000739::wuxiapptec.com > Sent: Sunday, June 07, 2009 12:53 PM > To: Warren DeLano > Subject: CCL: Do you have the experience about Stereo LCD monitor for > molecular modeling? >=20 >=20 > Sent to CCL by: "li_qiang_000739-x-wuxiapptec.com" [li_qiang_000739-x- > wuxiapptec.com] > Dear all, >=20 > Do you have the experience about Stereo LCD monitor for molecular > modeling? >=20 > We have a Samsung(r) SyncMaster 2233RZ 120 Hz LCD display, its resolution > is 1680x1050. The signal input is DVI-DL. >=20 > I try the LCD on one HP Xw6600 workstation with Quadro FX3700 graphics > card. The operation system is CentOS 5.3, so I update the latest nVidia > driver and set the xorg.conf with " Option "stereo" "3"". >=20 > But I can get the hardware stereo in our modeling software. >=20 > Who can tell me how to do it? Thank you for advance. >=20 > Best regards, >=20 > Li Qiang >=20 > CADD Laboratory > WUXI AppTec Co., Ltd. >=20 > E-mail: li_qiang_000739-.-wuxiapptec.com >=20 > Address: No.1 Building, 288 Fute Zhong Road, WaiGaoQiao Free > Trade Zone, Shanghai, P.R.China > PostCode: 200131 > Tel: 86-21-50463316 > Fax: 86-21-50461000 > Web Site: www.wuxiapptec.com >=20 >=20 >=20 > Save paper. Protect the environment. Print only when necessary. >=20 > This e-mail transmission may contain confidential or legally privileged > information belongs to WuXi AppTec Co., Ltd. The content of this > transmission is intended only for the individual or entity named in the e- > mail address. If you are not the intended recipient, you are hereby > notified that any disclosure, copying, distribution, or reliance upon the > content of this e-mail is strictly prohibited. >=20 > If you have received this e-mail transmission in error, please reply to > sender so that we can arrange correct delivery. Then please delete this > message from your inbox. >=20 >=20 >=20 > -=3Dhis is automatically added to each message by the mailing script = =3D>=20>=20>=20>=20>=20>=20>=20>=20>=20 >=20 >=20 >=20 >=20