From owner-chemistry@ccl.net Mon Mar 23 06:23:01 2009 From: "Gijs Schaftenaar schaft_+_cmbi.ru.nl" To: CCL Subject: CCL: International Computational Drug Discovery 2009 course Message-Id: <-38899-090323062051-15088-P0GL1OO8xxROfCAbCpILZA]^[server.ccl.net> X-Original-From: "Gijs Schaftenaar" Date: Mon, 23 Mar 2009 06:20:48 -0400 Sent to CCL by: "Gijs Schaftenaar" [schaft/a\cmbi.ru.nl] The International Computational Drug Discovery course will take place from June 29 - July 10 2009, at Nijmegen, The Netherlands. The course was developed by Computational Drug Discovery Group of the Centre of Molecular and Biomolecular Informatics (CMBI) of the Radboud University of Nijmegen in the Netherlands in collaboration with the pharmaceutical company Organon / Schering-Plough. The two-week course describes some of the recent advances in drug discovery informatics, with a focus on the application of e-science to real life problems. The course is targeted at MSc and PhD students, and postdocs, who are interested in the field of computational target and drug discovery. The fee for the course is 100 euro. The course is financially supported by the dutch funding agency NBIC. The Chemical Computing Group supports the course with educational licenses for their MOE software. For more information see the course website (http://www.cmbi.ru.nl/ICDD2009/) or the flyer (http://www.cmbi.ru.nl/ICDD-2009.pdf). Sincerely Yours, Dr. Gijs Schaftenaar Dr. Sander Nabuurs Prof. Jacob de Vlieg From owner-chemistry@ccl.net Mon Mar 23 09:00:01 2009 From: "yanli Wang ecustipp-$-163.com" To: CCL Subject: CCL: NICS====================================================== Message-Id: <-38900-090323021728-22500-1mjtrxUX6x2X9OnP/TlhRA*|*server.ccl.net> X-Original-From: "yanli Wang" Date: Mon, 23 Mar 2009 02:17:24 -0400 Sent to CCL by: "yanli Wang" [ecustipp[]163.com] ====================================================== Dear all, I have a question about NICS. I'd read references using NICS, but all applied to cyclic structures. Is it suitable to compute NICS to measure the aromaticity of non-cyclic aromatic compounds? such as "Y-aromaticy" compounds? Thanks very much! Yours Alice Wang ====================================================== From owner-chemistry@ccl.net Mon Mar 23 09:35:02 2009 From: "Joo Yun Lee jylee(!)krict.re.kr" To: CCL Subject: CCL:G: Gaussian input data include in Fe(III) Message-Id: <-38901-090320045508-14305-kecOJ/JMXe/AH/MruxudiA()server.ccl.net> X-Original-From: "Joo Yun Lee" Date: Fri, 20 Mar 2009 04:55:00 -0400 Sent to CCL by: "Joo Yun Lee" [jylee+*+krict.re.kr] Hello CCLers, I am trying to calculate optimization for C21H15N4SFe(III)complex using Gaussian03. Gaussian accept the number of total electrons to be (6x21)+(15)+(7x4)+(16)+(26)=211. However, I think 208 electrons due to oxidation state of Fe(III). According to the number of total electrons, multiplicity value is affected. ex) if the charge is 0, multiplicity(M) will be possible to be 2,4,or 6 in the case of total electrons 211, but other case of total electrons 208, M is possible to be 1,3,or 5. How can I include in the information about oxidation state of Fe(III)?? From owner-chemistry@ccl.net Mon Mar 23 10:10:00 2009 From: "elvis lee elvis.lee999{}hotmail.com" To: CCL Subject: CCL: RNA DOCKING Message-Id: <-38902-090323023002-23811-IhCkAlT4jLoABb9QFowPwg^^^server.ccl.net> X-Original-From: "elvis lee" Date: Mon, 23 Mar 2009 02:29:58 -0400 Sent to CCL by: "elvis lee" [elvis.lee999%%hotmail.com] Hi all, I am docking some ligand to RNAs receptors,but I am a stranger to this system and lots of problems confuse me ,even some common sense. 1.There are four kinds of oxygens connecting with backbone's phosphorus called O5',O3',OP2,OP1 in PDB atom name. My question is whether OP2 oxygen(single bond) retains hydrogen or not in the process of docking and how can I determin if OP2 oxygen keeps a unit of negtive charge. 2.Can I get some score function directing toward RNA system(free of charge and convenient) to rescore my docking poses and pick out correct poses from different docking poses? 3.Does anyone have any suggestion to RNA docking? How can I do precise docking to RNAs system? Thanks a lot in advance. elvis lee elvis.lee999],[hotmail.com ECUST,Shanghai,China From owner-chemistry@ccl.net Mon Mar 23 10:46:01 2009 From: "Nathanael Weill naweill() gmail.com" To: CCL Subject: CCL: PASS source Message-Id: <-38903-090323075518-15057-vVbHBel6tzNtxpHD/CYtqA]*[server.ccl.net> X-Original-From: "Nathanael Weill" Content-Language: fr Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 23 Mar 2009 12:06:46 +0100 MIME-Version: 1.0 Sent to CCL by: "Nathanael Weill" [naweill%%gmail.com] Many thanks!! It just need an old version of libstdc++ (2.8). I found a compatible = library and it's work fine. Thanks Nathanael Weill -----Message d'origine----- De=A0: owner-chemistry+naweill=3D=3Dgmail.com[a]ccl.net [mailto:owner-chemistry+naweill=3D=3Dgmail.com[a]ccl.net] De la part de = Vladimir Chupakhin chupvl^^^gmail.com Envoy=E9=A0: dimanche 22 mars 2009 21:10 =C0=A0: Weill, Nathanael Objet=A0: CCL: PASS source Sent to CCL by: Vladimir Chupakhin [chupvl-*-gmail.com] http://www.ccl.net/cca/software/UNIX/pass/overview.shtml here is the PASS page in CCL Vladimir Chupakhin nathanel weill naweill:_:gmail.com wrote: > Sent to CCL by: "nathanel weill" [naweill**gmail.com] > Dear CCLers, > I would like to use PASS program for cavity detection. On the = publication, it is mentionned that the source code should be freely avilable on ccl software repository. Unfortunately, I did nit find it... > Is someone still have the source code? > Thanks > Nathanael Weill> > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Mar 23 11:19:01 2009 From: "Saurabh Agrawal Saurabh.Agrawal:+:ucdconnect.ie" To: CCL Subject: CCL: RUTILE 110 SURFACE Message-Id: <-38904-090323100700-27399-4NIAWCQ6W/yXP7r60IP90w{:}server.ccl.net> X-Original-From: Saurabh Agrawal Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_+pf82aGE4a1+csph7luiGQ)" Date: Mon, 23 Mar 2009 13:06:42 +0000 (GMT) MIME-version: 1.0 Sent to CCL by: Saurabh Agrawal [Saurabh.Agrawal(~)ucdconnect.ie] This is a multi-part message in MIME format. --Boundary_(ID_+pf82aGE4a1+csph7luiGQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Dear CCL Subscribers, I am trying to make 110 rutile surface form the 1x1 lattice coordinat= es given below. I could replicate the surface using moe software. But= I am not sure which side of the surface is 110. Any information or t= utorial helpful to solve this problem would be of much help for me. HETATM=A0=A0=A0 1 TI=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 0.= 000=A0=A0 0.000=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0=A0=A0= =A0 TI=A0=20 HETATM=A0=A0=A0 2 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0= =A0 1.400=A0=A0 1.400=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 O=A0=20 HETATM=A0=A0=A0 3 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0 -1.= 400=A0 -1.400=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 O=A0=20 HETATM=A0=A0=A0 4 TI=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 2.= 296=A0=A0 2.296=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0=A0=A0= =A0 TI=A0=20 HETATM=A0=A0=A0 5 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0 -0.= 896=A0=A0 0.896=A0 -1.479=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 O=A0=20 HETATM=A0=A0=A0 6 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0= =A0 0.896=A0 -0.896=A0 -1.479=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 O=A0=20 END Thanking you in advance. Saurabh --Boundary_(ID_+pf82aGE4a1+csph7luiGQ) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Dear CCL Subscribers,

I am trying to make 110 rutile surface f= orm the 1x1 lattice coordinates given below. I could replicate the su= rface using moe software. But I am not sure which side of the surface= is 110. Any information or tutorial helpful to solve this problem wo= uld be of much help for me.


HETATM    1 TI&= nbsp;    *     1   =     0.000   0.000   0.000  1.= 00  0.00          T= I 
HETATM    2 O     = ; *     1       1.4= 00   1.400   0.000  1.00  0.00 &nb= sp;         O 
HETAT= M    3 O      *  &n= bsp;  1      -1.400  -1.400 &= nbsp; 0.000  1.00  0.00      =      O 
HETATM    4 TI&nb= sp;    *     1   &n= bsp;   2.296   2.296   0.000  1.00=   0.00          TI&= nbsp;
HETATM    5 O      = *     1      -0.896 = ;  0.896  -1.479  1.00  0.00   &nb= sp;       O 
HETATM  = ;  6 O      *     1=        0.896  -0.896  -1.479&= nbsp; 1.00  0.00        =    O 
END

Thanking you in advance.

S= aurabh
--Boundary_(ID_+pf82aGE4a1+csph7luiGQ)-- From owner-chemistry@ccl.net Mon Mar 23 11:54:01 2009 From: "Rajagopalan S. r.subramanian:ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: Gaussian input data include in Fe(III) Message-Id: <-38905-090323105112-31783-UGWA7olcgIvsdBin7CwE4Q,+,server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Mar 2009 15:50:58 +0100 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian|*|ipc.uni-stuttgart.de] Hi, What is the total charge of your complex. May be include the correct charge with mult. 2 or 4 or 6 normally should work (6 for HS and 2 for LS). bye Joo Yun Lee jylee(!)krict.re.kr wrote: > Sent to CCL by: "Joo Yun Lee" [jylee+*+krict.re.kr] > > Hello CCLers, > > I am trying to calculate optimization for C21H15N4SFe(III)complex using Gaussian03. > > Gaussian accept the number of total electrons to be (6x21)+(15)+(7x4)+(16)+(26)=211. > > However, I think 208 electrons due to oxidation state of Fe(III). > > According to the number of total electrons, multiplicity value is affected. > > ex) if the charge is 0, multiplicity(M) will be possible to be 2,4,or 6 in the case of total electrons 211, but other case of total electrons 208, M is possible to be 1,3,or 5. > > How can I include in the information about oxidation state of Fe(III)??> > > From owner-chemistry@ccl.net Mon Mar 23 12:29:00 2009 From: "Marcel Swart marcel.swart[]icrea.es" To: CCL Subject: CCL:G: Gaussian input data include in Fe(III) Message-Id: <-38906-090323104130-24177-38Pe7fmOgiRS0g/8Q3xFcw:_:server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-7--333459246 Date: Mon, 23 Mar 2009 15:41:02 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart++icrea.es] --Apple-Mail-7--333459246 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed You should give the charge and multiplicity of your system on the line before the coordinates. 0 1 means total charge 0, singlet state If your ligands do not carry charge (and thus the total charge is +3): for singlet: 3 1 for triplet: 3 3 for quintuplet: 3 5 On Mar 20, 2009, at 9:55 AM, Joo Yun Lee jylee(!)krict.re.kr wrote: > Hello CCLers, > > I am trying to calculate optimization for C21H15N4SFe(III)complex =20 > using Gaussian03. > > Gaussian accept the number of total electrons to be (6x21)+(15)=20 > +(7x4)+(16)+(26)=3D211. > > However, I think 208 electrons due to oxidation state of Fe(III). > > According to the number of total electrons, multiplicity value is =20 > affected. > > ex) if the charge is 0, multiplicity(M) will be possible to be =20 > 2,4,or 6 in the case of total electrons 211, but other case of =20 > total electrons 208, M is possible to be 1,3,or 5. > > How can I include in the information about oxidation state of Fe=20 > (III)?? =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart/./icrea.es marcel.swart/./udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-7--333459246 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 You should give the charge and multiplicity of your system on the = line
before the coordinates.
0 1
means total = charge 0, singlet state

If your ligands do not = carry charge (and thus the total charge is = +3):

for singlet:
3 = 1
for triplet:
3 3
for = quintuplet:
3 = 5

On Mar 20, 2009, at = 9:55 AM, Joo Yun Lee jylee(!)krict.re.kr wrote:

Hello CCLers,


I = am trying to calculate optimization for C21H15N4SFe(III)complex using = Gaussian03.


Gaussian accept the number of total electrons to be = (6x21)+(15)+(7x4)+(16)+(26)=3D211.


However, I think 208 electrons due to = oxidation state of Fe(III).


According to the number of total = electrons, multiplicity value is affected.


ex) if the = charge is 0, multiplicity(M) will be possible to be 2,4,or 6 in the case = of total electrons 211, but other case of total electrons 208, M is = possible to be 1,3,or 5.


How can I include in the information = about oxidation state of Fe(III)??

=

dr. Marcel = Swart

ICREA = researcher at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
17003 Girona
Catalunya = (Spain)

tel
marcel.swart/./udg.edu



=

= --Apple-Mail-7--333459246-- From owner-chemistry@ccl.net Mon Mar 23 13:04:00 2009 From: "Johannes Hachmann jh388]_[cornell.edu" To: CCL Subject: CCL:G: Gaussian input data include in Fe(III) Message-Id: <-38907-090323104937-30553-u9tGJiZjnb+6cnPNmzyCHA%x%server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Mar 2009 10:49:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388.*.cornell.edu] Hi, charge of your overall molecule can be changed in the charge/multiplicity line, right before your geometry input. For these basic things you should first check out e.g. the g03 online manual... HOWEVER, BE CAREFUL! Are you sure your OVERALL complex is charged 3+? If not, that means that your Fe(III) electron count is balanced by a negatively charged ligand! Best Johannes --------------------------------------------------------------- Johannes Hachmann Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu*ccl.net > [mailto:owner-chemistry+jh388==cornell.edu*ccl.net] On Behalf > Of Joo Yun Lee jylee(!)krict.re.kr > Sent: Friday, March 20, 2009 4:55 AM > To: Hachmann, Johannes > Subject: CCL:G: Gaussian input data include in Fe(III) > > > Sent to CCL by: "Joo Yun Lee" [jylee+*+krict.re.kr] > > Hello CCLers, > > I am trying to calculate optimization for > C21H15N4SFe(III)complex using Gaussian03. > > Gaussian accept the number of total electrons to be > (6x21)+(15)+(7x4)+(16)+(26)=211. > > However, I think 208 electrons due to oxidation state of Fe(III). > > According to the number of total electrons, multiplicity > value is affected. > > ex) if the charge is 0, multiplicity(M) will be possible to > be 2,4,or 6 in the case of total electrons 211, but other > case of total electrons 208, M is possible to be 1,3,or 5. > > How can I include in the information about oxidation state of > Fe(III)?? > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the * sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Mon Mar 23 13:40:01 2009 From: "Anthony D DeBellis anthony.debellis_-_ciba.com" To: CCL Subject: CCL: Active site mimics Message-Id: <-38908-090323110854-16000-p6aXGvYBHq/1KgFeroNVtA+*+server.ccl.net> X-Original-From: "Anthony D DeBellis" Date: Mon, 23 Mar 2009 11:08:49 -0400 Sent to CCL by: "Anthony D DeBellis" [anthony.debellis_._ciba.com] Pardon my ignorance in this area, but is anyone aware of work (experimental or computational) that has been done to attempt to mimic the "active site" of a peptide or enzyme with a synthetic oligomer or polymer? By synthetic polymer I mean one that is composed of common or industrially relevant monomers. Anthony DeBellis Ciba anthony.debellis!=!ciba.com From owner-chemistry@ccl.net Mon Mar 23 14:14:01 2009 From: "Johannes Hachmann jh388{}cornell.edu" To: CCL Subject: CCL:G: (correction) Energy change upon swapping two orbitals in Gaussian 98 Message-Id: <-38909-090323110805-15657-NH8x1V7EVdyEWGFmzTqLiw#%#server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Mar 2009 11:07:47 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388() cornell.edu] Dear Yutao, > It seems that this SCF is extremely sensitive, any minor > change is sufficient to lead to a different solution. But I'm > very curious what could be the reason? The iron? At least the > frontier orbital energies don't seem to be very close: Transition metal calcs are a bit tricky - you could argue that the problems one finds with multiple electronic minima is a reflection of the great chemical diversity of transition metal compounds. That's why it is in my eyes particularly important to double check every output one gets with a lot of scrutiny for potential errors - they can just occur so easily... > I didn't use Guess=Mix and the symmetry doesn't seem to be a > problem, since the structure is highly asymmetric and the > point group is actually C1 through all calculations. Be careful here: The Guess=Mix not only breaks spatial symmetry but in particular also spin symmetry, which is important if you want to get a proper unrestricted solution! Best Johannes --------------------------------------------------------------- Johannes Hachmann Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu]~[ccl.net > [mailto:owner-chemistry+jh388==cornell.edu]~[ccl.net] On Behalf > Of Yutao Yue yutao.yue%x%gmail.com > Sent: Sunday, March 22, 2009 7:22 PM > To: Hachmann, Johannes > Subject: CCL:G: (correction) Energy change upon swapping two > orbitals in Gaussian 98 > > Thanks dear friend, I've done what you suggested. The G98 job > just got executed and finished, and arrived at a result > that's almost identical to the swapped result (with lower energy)! > > I didn't use Guess=Mix and the symmetry doesn't seem to be a > problem, since the structure is highly asymmetric and the > point group is actually C1 through all calculations. > > What also happened is that, if I use the swapped result as > initial guess, to do exactly the same SCF calculation using > Guess=Read (NOT swapping back the orbitals), I arrived at > another solution with an energy higher than the "swapped > solution" but lower than the original solution. Ideally this > should not happen because it starts with a good initial guess > (with lower energy) and finishes at a bad solution (higher energy). > > It seems that this SCF is extremely sensitive, any minor > change is sufficient to lead to a different solution. But I'm > very curious what could be the reason? The iron? At least the > frontier orbital energies don't seem to be very close: > > Energy E=-3295.07657288 > NBO Fe Q=1.46819 S=3.67069 > S**2 guess= 6.0137 6.0163 > > 166 -0.02694 > 167 0.00934 > Alpha HOMO is MO # 167 > 168 0.01592 > > 161 -0.02639 > 162 0.00532 > 163 0.01207 > Beta HOMO is MO # 163 > 164 0.01835 > > > Best, > Yutao > > > On Fri, Mar 13, 2009 at 3:47 AM, Johannes Hachmann jh388 a > cornell.edu wrote: > > > > Sent to CCL by: "Johannes Hachmann" [jh388/a\cornell.edu] > Dear Yutao, > > it's hard to say what exactly is going on without a > closer look, but if the > calc doesn't take too long, try something like > > # UBLYP/6-31g(d) POP=FULL GFPRINT GFOLDPRINT SYMM=LOOSE > GUESS=READ > INT=ULTRAFINE STABLE=OPT > > That will take care of potential threshold and > instability issues and you > can compare the result to your swap result. Did you use > GUESS=MIX in your > very first calc? If not, a high symmetry guess might > have led you to an > instability. I am however a bit surprised that a swap > within the occupied > orbs helped... > > Best > > Johannes > > --------------------------------------------------------------- > Johannes Hachmann > > Chan Research Group > 140D Baker Laboratory > Department of Chemistry and Chemical Biology > Cornell University > Ithaca, NY 14853-1301 > USA > --------------------------------------------------------------- > > > -----Original Message----- > > From: owner-chemistry+jh388==cornell.edu-,-ccl.net > > [mailto:owner-chemistry+jh388 > ==cornell.edu-,-ccl.net] On Behalf > > Of Yutao Yue yutao.yue:-:gmail.com > > Sent: Thursday, March 12, 2009 3:16 PM > > To: Hachmann, Johannes > > Subject: CCL:G: (correction) Energy change upon swapping two > > orbitals in Gaussian 98 > > > > Thank you very much Johannes, I did swap the two highest > > OCCUPIED beta orbitals. I was also doubting that the original > > solution was not stable. I compared the solutions before and > > after swapping, the MO compositions are almost identical for > > frontier orbitals, and only some minor differences for some > > deeper orbitals. Plus, the S2 values, the NBO charges and > > spins of some characteristic atoms (metal, etc) are almost > > exactly the same, up to quite a few digits. > > > > On the other hand, although with highly similar MO > > compositions, the MO energy themselves are fairly different > > through all MOs including the deepest, e.g., the difference > > for a single MO is on the order of 0.01 a.u.. > > > > By the way, I used the default SCF convergence level (which > > is equivalent to conver=4). But I guess that's far from > > introducing errors of this magnitude right? > > > > I wonder is it possible that Gaussian does something > > artificial (and arbitrary? because in one case energy went up > > and the other case it went down) to the MO energies, once the > > initial guess swapping is introduced? > > > > Regards, > > Yutao > > > > > > On Thu, Mar 12, 2009 at 12:50 PM, Johannes Hachmann > > jh388~!~cornell.edu wrote: > > > > > > > > Sent to CCL by: "Johannes Hachmann" > [jh388]*[cornell.edu] > > Dear Yutao, > > > > sounds to me like you might have landed on an > > electronic instability the > > first time. SCF for (transition-)metal compounds can be > > very hard to > > converge. Try STABLE=OPT starting from your original > > calc without the > > orbital swap and see whether that lowers the energy (in > > that case, your swap > > has introduced some mixing/symmetry breaking and led to > > a more stable > > state). You can check the S2 value of your two results > > to see, whether your > > state has changed. You might also want to check your > > SCF convergence > > threshold and DFT grid (although it should not make a > > difference of 20mH). > > > > Generally, swapping the highest two HOMOs should not > > change the energy at > > all, but maybe you ment the HOMO-LUMO pair? A vanishing > > HOMO-LUMO gap > > indicates a system with nondynamic correlation, and you > > might not want to > > use a single reference method like DFT in the > first place. > > > > Hope that helps. Best > > > > Johannes > > > > > --------------------------------------------------------------- > > Johannes Hachmann > > > > Chan Research Group > > 140D Baker Laboratory > > Department of Chemistry and Chemical Biology > > Cornell University > > Ithaca, NY 14853-1301 > > USA > > > --------------------------------------------------------------- > > > > > > > > > > > -----Original Message----- > > > From: owner-chemistry+jh388==cornell.edu-.-ccl.net > > > [mailto:owner-chemistry+jh388 > > > > ==cornell.edu-.-ccl.net] > On Behalf > > > Of Yutao Yue Yutao.Yue#,#gmail.com > > > Sent: Thursday, March 12, 2009 10:55 AM > > > To: Hachmann, Johannes > > > Subject: CCL:G: (correction) Energy change > upon swapping two > > > orbitals in Gaussian 98 > > > > > > > > > Sent to CCL by: "Yutao Yue" [Yutao.Yue- > -gmail.com] (sorry > > > the energy changes are 0.02 a.u., NOT 0.2 a.u.) > > > > > > Dear All, > > > > > > I have a successful G98 single point calculation > > > (UBLYP/6-31G*) on a metal-containing system > of around 70 > > > atoms. I use the result MOs as initial guess, > but swapped the > > > two highest occupied beta orbitals (which are > supposed to be > > > highly competing with each other) upon > reading in the initial > > > guess, to do another G98 single point > calculation on the same > > > system. I then arrived at a solution that, > the frontier > > > orbitals are almost identical to the original solution > > > including the ordering of the beta orbitals, > while the single > > > point energy is 0.02 a.u. lower! > > > > > > Similar calculations was done with > UBPW91/6-31G*, and again > > > the orbitals go back to original ordering, > but the single > > > point energy is 0.02 a.u. higher now! > > > > > > Anybody have any idea about those energy changes? > > > > > > Thanks a lot and wish everybody a nice day! > > > > > > -Yutao Yue > > > > > > > > > > > > -= This is automatically added to each > message by the mailing > > > script =- To recover the email address of the > author of the > > > message, please change the strange characters > on the top line > > > to the -.- sign. You can also look up the > > X-Original-From: line > > > > > in the mail header.> Conferences: > > > > > > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > > > > > > -= 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 use> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > Search Messages: > > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > > > > > > > > > > > > -= This is automatically added to each message by the > mailing script =- > > > > E-mail to subscribers: CHEMISTRY!=cl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST!=cl.net or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > > > From owner-chemistry@ccl.net Mon Mar 23 14:51:01 2009 From: "Sebastian Radestock sebastian|a|radestock.net" To: CCL Subject: CCL: [Fwd: CCL: RNA DOCKING] Message-Id: <-38910-090323115129-14436-EsNfr6an51/cN72tvjlIVA .. server.ccl.net> X-Original-From: Sebastian Radestock Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 23 Mar 2009 16:51:13 +0100 MIME-Version: 1.0 Sent to CCL by: Sebastian Radestock [sebastian{=}radestock.net] Dear Elvis, > 2.Can I get some score function directing toward RNA system(free of charg= e > and convenient) to rescore my docking poses and pick out correct poses > from different docking poses? > > 3.Does anyone have any suggestion to RNA docking? How can I do precise > docking to RNAs system? For docking ligands to RNA molecules you might use DrugScore_RNA. DrugScore_RNA is a knowledge-based scoring function. DrugScore has been used as a function for re-scoring receptor-ligand complexes, and it has been adapted to be used as an energy function in docking with AutoDock. Here are some references of interest: * Pfeffer, P., Gohlke, H. DrugScore_RNA - Knowledge-based scoring function to predict RNA-ligand interactions. J. Chem. Inf. Model. 2007, 47, 1868-1876. * Radestock, S., Boehm, M., Gohlke, H. Improving Binding Mode Predictions by Docking into Protein-Specifically Adapted Potential Fields. J. Med. Chem. 2005, 48, 5466 - 5479. * Sotriffer, C. A., Gohlke, H., Klebe, G. Docking into knowledge-based potential fields: A comparative evaluation of DrugScore. J. Med. Chem. 2002, 45, 1967-1970. Kind regards, Sebastian. --=20 Sebastian Radestock, Dipl.-Bioinformatiker Computational Pharmaceutical Chemistry Christian-Albrechts-Universit=E4t zu Kiel URL: http://www.radestock.net Mail: sebastian]|[radestock.net From owner-chemistry@ccl.net Mon Mar 23 15:24:01 2009 From: "Close, David M. CLOSED%mail.etsu.edu" To: CCL Subject: CCL: RUTILE 110 SURFACE Message-Id: <-38911-090323135323-16272-Qi57K9xbAC+fi1kKRkRLfw:-:server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C9ABD4.B43946F8" Date: Mon, 23 Mar 2009 12:30:42 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED|-|mail.etsu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C9ABD4.B43946F8 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Saurabh: You need to look in a book on crystallography. Rutile forms in tetragonal prisms. The plane you want (1,1,0) is the cleavage plane. Anyway, these three numbers are the Miller indices. The plane you are looking for is one full lattice spacing in the a-direction, one full lattice spacing in the b-direction, an no displacement in the c-direction. If you have access to an elementary graphics program, you can input the coordinates you supplied, the lattice constants you supplied, and the program will draw the unit cell. From this you can determine the cleavage plane. Regards, Dave Close. =20 > From: owner-chemistry+closed=3D=3Detsu.edu.:-:.ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu.:-:.ccl.net] On Behalf Of = Saurabh Agrawal Saurabh.Agrawal:+:ucdconnect.ie Sent: Monday, March 23, 2009 9:07 AM To: Close, David M. Subject: CCL: RUTILE 110 SURFACE =20 Dear CCL Subscribers, I am trying to make 110 rutile surface form the 1x1 lattice coordinates given below. I could replicate the surface using moe software. But I am not sure which side of the surface is 110. Any information or tutorial helpful to solve this problem would be of much help for me. HETATM 1 TI * 1 0.000 0.000 0.000 1.00 0.00 TI =20 HETATM 2 O * 1 1.400 1.400 0.000 1.00 0.00 O =20 HETATM 3 O * 1 -1.400 -1.400 0.000 1.00 0.00 O =20 HETATM 4 TI * 1 2.296 2.296 0.000 1.00 0.00 TI =20 HETATM 5 O * 1 -0.896 0.896 -1.479 1.00 0.00 O =20 HETATM 6 O * 1 0.896 -0.896 -1.479 1.00 0.00 O =20 END Thanking you in advance. Saurabh ------_=_NextPart_001_01C9ABD4.B43946F8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Saurabh:

  You need to look in a book on = crystallography.  Rutile forms in tetragonal prisms.  The plane you want (1,1,0) is = the cleavage plane.

Anyway, these three numbers are the Miller indices. =   The plane you are looking for is one full lattice spacing in the = a-direction, one full lattice spacing in the b-direction, an no displacement in the = c-direction. If you have access to an elementary graphics program, you can input the coordinates you supplied, the lattice constants you supplied, and the = program will draw the unit cell.  From this you can determine the cleavage = plane.

  Regards, Dave Close.

 

From:= = owner-chemistry+closed=3D=3Detsu.edu.:-:.ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu.:-:.ccl.net] On Behalf Of = Saurabh Agrawal Saurabh.Agrawal:+:ucdconnect.ie
Sent: Monday, March 23, 2009 9:07 AM
To: Close, David M.
Subject: CCL: RUTILE 110 SURFACE

 

Dear CCL Subscribers,

I am trying to make 110 rutile surface form the 1x1 lattice coordinates = given below. I could replicate the surface using moe software. But I am not = sure which side of the surface is 110. Any information or tutorial helpful to = solve this problem would be of much help for me.


HETATM    1 TI     = *     1       0.000   = 0.000   0.000  1.00  0.00          TI 
HETATM    2 O      *     1       1.400   1.400   0.000  1.00  0.00           O  =
HETATM    3 O      *     1      -1.400  -1.400   0.000  1.00  0.00           O  =
HETATM    4 TI     = *     1       2.296   = 2.296   0.000  1.00  0.00          TI 
HETATM    5 O      *     1      = -0.896   0.896  -1.479  1.00  0.00           O  =
HETATM    6 O      *     1       = 0.896  -0.896  -1.479  1.00  0.00           O  =
END

Thanking you in advance.

Saurabh

------_=_NextPart_001_01C9ABD4.B43946F8-- From owner-chemistry@ccl.net Mon Mar 23 16:44:01 2009 From: "gungun lin lingungun*|*163.com" To: CCL Subject: CCL:G: about l502.exe error Message-Id: <-38912-090323164202-19951-oi5U55ZMI6MpbsYRzXcN3w%server.ccl.net> X-Original-From: "gungun lin" Date: Mon, 23 Mar 2009 16:41:58 -0400 Sent to CCL by: "gungun lin" [lingungun##163.com] Hi, all: i have solved the problem l103.exe error with the suggestions by Ol Ga and Denis. but now i have faced a new problem which obsessed me a whole day. my input file: %chk=gxx %mem=45Mw #p blyp/3-21G PBC(NCELLMAX=5) Opt guess=huckel test B4C_opt 0 1 B 1.39299950 0.16527989 0.98934499 B 3.53523620 2.27856625 4.07031887 B 5.61169657 1.33690423 0.98934499 B 3.85967682 4.76768131 3.52821203 B 5.93613719 1.54601599 3.52821203 B 5.93613719 3.82601929 0.44723814 B 3.91723980 0.85288810 2.37939728 B 3.91723980 2.52477908 0.12016702 B 2.39460368 3.21528520 2.37939728 B 7.07676972 2.88930034 2.13815973 B 5.55413360 5.25169744 2.13815973 B 5.55413360 3.57980646 4.39739000 C 3.64647876 2.35026543 1.73925945 C 5.82489464 3.75432011 2.77829756 C 4.73568670 3.05229277 2.25877851 tv 5.18690000 0.00000000 0.00000000 tv 2.14223670 4.72384944 0.00000000 tv 2.14223670 1.38073610 4.51755701 the error comes out as : One-electron integrals computed using PRISM. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 2.00D-06. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 4.00D-06. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 8.00D-06. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 1.60D-05. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 3.20D-05. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 6.40D-05. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 1.28D-04. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 2.56D-04. Error in orthogonal basis= 2.00D+00 with 135 functions, increasing threshold to 5.12D-04. Error in orthogonal basis= 2.00D+00 with 134 functions, increasing threshold to 1.02D-03. Error in orthogonal basis= 2.00D+00 with 134 functions, increasing threshold to 2.05D-03. Error in orthogonal basis= 2.00D+00 with 134 functions, increasing threshold to 4.10D-03. Error in orthogonal basis= 2.00D+00 with 133 functions, increasing threshold to 8.19D-03. Error in orthogonal basis= 2.00D+00 with 129 functions, increasing threshold to 1.64D-02. Error in orthogonal basis= 2.00D+00 with 126 functions, increasing threshold to 3.28D-02. Error in orthogonal basis= 2.00D+00 with 122 functions, increasing threshold to 6.55D-02. Error in orthogonal basis= 2.00D+00 with 115 functions, increasing threshold to 1.31D-01. Error in orthogonal basis= 2.00D+00 with 109 functions, increasing threshold to 2.62D-01. Error in orthogonal basis= 2.00D+00 with 93 functions, increasing threshold to 5.24D-01. Error in orthogonal basis= 2.00D+00 with 74 functions, increasing threshold to 1.05D+00. NBasis= 135 RedAO= T NBF= 135 NBsUse= 41 1.05D+00 NBFU= 41 Precomputing XC quadrature grid using IXCGrd= 2 IRadAn= 0 IRanWt= -1 IRanGd= 0. RepCel: MaxNCR= 5 NClRep= 5 NMtPBC= 5. NRdTot= 899 NPtTot= 113974 NUsed= 118171 NTot= 118187 NSgBfM= 621 621 621 621. Leave Link 302 at Mon Mar 23 21:22:17 2009, MaxMem= 47185920 cpu: 23.0 (Enter C:\G03W\l303.exe) DipDrv: MaxL=1. Leave Link 303 at Mon Mar 23 21:22:18 2009, MaxMem= 47185920 cpu: 0.0 (Enter C:\G03W\l401.exe) Projected New-EHT guess. Enter ItEHT: IZDO=4 IZDPar=0 Conv= 1.00D-06 N= 60 It= 1 EEH= -139.283897490 EQH= 0.000000000000E+00 EH= -139.283897490 Leave Link 401 at Mon Mar 23 21:22:18 2009, MaxMem= 47185920 cpu: 0.0 (Enter C:\G03W\l502.exe) Closed shell SCF: Requested convergence on RMS density matrix=1.00D-07 within 128 cycles. Requested convergence on MAX density matrix=1.00D-05. Requested convergence on energy=1.00D-05. No special actions if energy rises. Using DIIS extrapolation, IDIIS= 1040. NCelOv= 5 NClRep= 5 NMtPBC= 5 NRecip= 686 NKPnt= 500. Two-electron integral symmetry not used. 118170 words used for storage of precomputed grid. IEnd= 573985 IEndB= 573985 NGot= 47185920 MDV= 46757098 LenX= 46757098 Threshold for overlap eigenvalues 1.000D-06 Ratio Low Low Low Low Low High Min 5.771D-06 7.6D+00 6.5D+00 5.9D+00 5.5D+00 4.7D+00 4.5D-05 Max 3.328D-04 8.5D+00 7.5D+00 6.8D+00 6.0D+00 5.8D+00 2.7D-03 S in ortho basis: MxErrOnDiag= 0.2000D+01 MxErrOfDiag= 0.3901D-10 Cycle 1 Pass 1 IDiag 1: FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=F KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 4 Number of levels for PrismC: 2 RepCel: MaxNCR= 5 NClRep= 5 NMtPBC= 5. Spurious integrated density or basis function: NE= 78 NElCor= 0 El error=1.98D-01 rel=2.54D-03 Tolerance=1.00D-03 Shell 18 absolute error=3.64D-02 Tolerance=1.20D-02 Shell 3 signed error=3.06D-02 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in C:\G03W\l502.exe at Mon Mar 23 21:33:27 2009. Job cpu time: 0 days 0 hours 11 minutes 48.0 seconds. File lengths (MBytes): RWF= 265 Int= 0 D2E= 0 Chk= 1 Scr= 1 --------------------------------------------------------- your suggestions will be appreciated! thanks a lot! From owner-chemistry@ccl.net Mon Mar 23 17:22:00 2009 From: "Ryszard Czerminski ryszard.czerminski-,-astrazeneca.com" To: CCL Subject: CCL: QSAR software Message-Id: <-38913-090323165255-24550-joc6O4FfksehdL8CWzcl7w*server.ccl.net> X-Original-From: "Ryszard Czerminski" Date: Mon, 23 Mar 2009 16:52:52 -0400 Sent to CCL by: "Ryszard Czerminski" [ryszard.czerminski**astrazeneca.com] One more try. We have some code that generates 3D QSAR descriptors, which can be downloaded from http://pubs.acs.org/doi/suppl/10.1021/ci800009u. It uses the OEchem library, which can be obtained free for academic use from OpenEye (http://www.eyeopen.com). Note that the code doesn't do molecular alignment. OpeneEye's ROCS might come in handy for that or you may want to use your other prefered approach. We've had good luck with R for model fitting (http://www.r-project.org/) using PLS, SVM and randomForest. Good luck, Ryszard From owner-chemistry@ccl.net Mon Mar 23 18:11:00 2009 From: "Roland Stote rstote~~chimie.u-strasbg.fr" To: CCL Subject: CCL: Reminder: Meeting of the GGMM May 5-7, 2009 Mittelwihr, Alsace France Message-Id: <-38914-090323174618-28850-HX2su8UDB0Lv7A0T9JAJIA[]server.ccl.net> X-Original-From: "Roland Stote" Date: Mon, 23 Mar 2009 17:46:13 -0400 Sent to CCL by: "Roland Stote" [rstote:_:chimie.u-strasbg.fr] Dear Colleagues, The thematic Group of Graphics and Molecular Modeling (GGMM) is organizing its 16th congress from May 5 to 7, 2009 in Mittelwihr (Alsace), France. The program is accessible online at http://ggmm2009.u-strasbg.fr/conference/program.html ** PLEASE NOTE THAT THIS CONFERENCE IS CONDUCTED IN FRENCH ** This meeting is oriented toward the international French speaking computational community and it brings together between 100 and 150 researchers from the public and industrial domains. The program includes plenary lectures, oral communications and poster presentations. The objective of the meeting is to address advances in the area of molecular simulations and their application to complex systems. The themes covered in this year's meeting concern simulations of nucleic acids, proteins, sugars, membranes, as well as molecular interactions applied to pharmacology and supramolecular systems. The organizing committee, Annick Dejaegere, Pascal Auffinger, Joerg Baschnagel, Martin Spichty, Roland Stote and Antoine Taly