From owner-chemistry@ccl.net Wed Jul 7 08:14:00 2010 From: "Kuhn Liu nature.like|*|gmail.com" To: CCL Subject: CCL:G: How to calculate Einstein A coefficient by Gaussian program Message-Id: <-42252-100707072111-6131-tU4U4YUR734TGvaTKHH6Ng[A]server.ccl.net> X-Original-From: "Kuhn Liu" Date: Wed, 7 Jul 2010 07:21:10 -0400 Sent to CCL by: "Kuhn Liu" [nature.like(-)gmail.com] We want to calculate the Einstein A coefficient (Spontaneous emission rate) of a molecular vibrational mode. Its unit is S-1. When we do frequency analysis by Gaussian program, we can get the vibrational frequency and Infrared Intensity (Unit: KM Mole-1). Now the qustions are: 1) Is there any the relationship with Einstein A coefficient and Infrared Intensity ? 2) How can we calcualte Einstein A coefficient by Gaussian Program? Thanks a lot. Kuhn. nature.like _ gmail.com From owner-chemistry@ccl.net Wed Jul 7 08:49:00 2010 From: "FyD fyd!=!q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Release of the R.E.D.-III.4 tools Message-Id: <-42253-100707030445-30728-EjjkVOMaJJhYl8vZB4KiOw::server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 07 Jul 2010 09:04:36 +0200 MIME-Version: 1.0 Sent to CCL by: FyD [fyd]~[q4md-forcefieldtools.org] Dear All, I am pleased to announce the release of the program RESP ESP charge Derive version III.4 (or R.E.D. III.4) and its related tools (Ante_R.E.D.-1.4 and X R.E.D. III.4) available ]![ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections and code cleaning in R.E.D. III.3, - Development of the Mini-Howto, - Tutorials have been updated, - Charge reproducibility has been further developed: the rigid-body reorientation algorithm has been re-written allowing all users to differentiate translation, rotation from the original reorientation approach, - Cartesian coordinates of molecular fragments originating from molecular fusion between two molecules are now recalculated allowing to generate correct geometries. The R.E.D. III.4 tools are now distributed under the GNU General Public License after a simple Register & Download procedure. The article describing the R.E.D. Tools is now available ]![ http://www.rsc.org/publishing/journals/CP/article.asp?doi=c0cp00111b News about the latest developments of R.E.D. IV can be found ]![ http://q4md-forcefieldtools.org/RED/popup/news.php. RESP and ESP charge derivation for a new structure is an important step in molecular dynamics simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields. To derive such atom-centered charges three steps need to be followed: - First, the molecule studied is optimized to determine a stable minimum (using a quantum chemistry software). - Then, this minimized structure is used to calculate a Molecular Electrostatic Potential (MEP) on a three-dimensional grid (using again a quantum chemistry software). - Finally, this grid is exported into the 'RESP program' (also downloadable from the CCL software database or from q4md-forcefieldtools) which is used to fit atom-centered charges to the MEP. Although this method is now used 'routinely' to obtain partial charges for molecules, in our opinion, it suffers from a number of limitations: - To apply this strategy, which requires the described above steps but also numerous format conversions between the different programs used, a significant number of scripts, programs and compilers are needed and used sequentially. Consequently, the procedure is tedious, time-consuming, and numerous errors can be introduced without having a real way to check them. - Although it is admitted that any quantum chemistry programs could be used to minimize the starting structure and to calculate the MEP, the 'Amber' developers mainly use the 'Gaussian' program, which is a proprietary software. The 'GAMESS' academic program, which is provided at no cost and which provide similar functionality for 'RESP' and 'ESP' charges development than 'Gaussian', is not officially used to derive 'RESP' or 'ESP' charges. Indeed, it is known that partial charges calculated using 'GAMESS', are 'different' than those determined using 'Gaussian'. - Finally, starting from different sets of Cartesian coordinates for a same molecule, the 'RESP' or 'ESP' partial charges are, in somes cases, not reproducible even using 'Gaussian', making errors in the protocol difficult to detect. Thus, we developed the R.E.D. I (RESP ESP charge Derive, version 1.0) program to automatically derive 'RESP' and 'ESP' charges starting from an un-optimized PDB structure. R.E.D. sequentially executes (i) either the 'GAMESS' program or the 'Gaussian' program to minimize the target structure and to compute the corresponding MEP, and (ii) the 'RESP' program to fit the atom-centered charges to the grid previously determined. Format conversions needed during the procedure and 'GAMESS', 'Gaussian' and 'RESP' inputs are automatically generated by R.E.D. By controlling the molecular orientation of the optimized geometry, a new RESP fitting procedure based on multi-orientation feature is proposed and results in highly reproducible 'RESP' and 'ESP' charges independently of the QM software or the initial Cartesian coordinate set. With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has been implemented. Such an approach permits to make the atom charge values more 'general', and is useful in molecular dynamics simulations where the whole conformational space needs to be explored. Thus with R.E.D.-II, 'multi-conformation' and 'multi-orientation' RESP fit can be performed together or independently according to the user choice. 'Standard' but also 'non-standard' RESP inputs can also be generated. Finally, RESP and ESP charges can be derived for chemical elements having up to a total number of electrons, Z = 35. With R.E.D. III.x (version 3.x), the control of charge constraints for atoms and groups of atoms in a molecule (intra-molecule charge constraint) or between two molecules (inter-molecule charge constraint and inter-molecular charge equivalencing) has been incorporated allowing for the derivation of the RESP and ESP atom charge values for molecule fragments and sets of molecules. Fitting procedures involving multiple molecules, and for each molecule, multiple conformations, and for each conformation, multiple orientations, can now be automatically carried out. Moverover, eight different charge derivation procedures using different MEP computation algorithms (Connolly surface and CHELPG algorithms) and different fitting procedures (with or without hyperbolic restraints) are now available. Potentially, an infinite number of approaches can be developed by simply changing a few words in the R.E.D. III.x source code. Such procedures can be used in simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields. Once the R.E.D. execution is completed, the charge values are available in Tripos mol2 file(s) which can be considered as precursors of AMBER OFF and CHARMM RFT or PSF force field libraries. R.E.D. makes the development of the 'RESP' and 'ESP' charges a straightforward, simple and highly reliable procedure. R.E.D. interfaces the GAMESS-US or Gaussian program and RESP program. R.E.D. III.x is now fully compatible with GAMESS-US (and its WinGAMESS version), Firefly and the Gaussian 1994, 1998, 2003 and 2009 versions on UNIX, MacIntosh and Windows plateforms. R.E.D. III.x is distributed with two other programs: - X R.E.D. is a graphical user-friendly interface, which has been developed to graphically execute R.E.D. and modify R.E.D. variables. - Ante_R.E.D. is a program useful for preparing R.E.D. inputs, and in particular the 'P2N' files. The P2N file format is a new file format introduced with R.E.D. III. It corresponds to the PDB file format with a second column of atom names. R.E.D. III.x, Ante_R.E.D.-1.x, and X R.E.D. III.x constitute the R.E.D. III.x tools. R.E.D. (versions I, II and III.x) and Ante_R.E.D. have been written with the 'Perl' programming language (See also the O'REILLY web site), while X R.E.D. has been developed using the 'tcl/tk' programming language. 'Perl' and 'tcl/tk' are interpreted programming languages, meaning that the programs written with these languages do not need to be compiled. This makes R.E.D., Ante_R.E.D. and X R.E.D. simple to use, highly flexible and portable. They are fully functional on UNIX, MacIntosh and Windows plateforms. The R.E.D. III.4 tools are now distributed under the GNU General Public License after a simple Register & Download procedure. If you have questions about the R.E.D. III.x tools, please, first check the documentation available (i. e. the manuals and FAQ). Basic tutorials are available in the R.E.D. I and R.E.D. II manuals, and new Tutorials have been written to describe Ante_R.E.D.-1.x, R.E.D. III.x and also R.E.DD.B.. If you need help about using the R.E.D. III.x tools, a general public help is now provided with the q4md-forcefieldtools mailing list. Any researcher can participate in this mailing list by answering and/or sending queries at q4md-fft]![q4md-forcefieldtools.org after registration at sympa]![q4md-forcefieldtools.org. To register in the q4md-fft mailing list just send an email to sympa]![q4md-forcefieldtools.org with 'subscribe q4md-fft' in the email subject or body (to un-subscribe just send 'unsubscribe q4md-fft'). Archives of the q4md-fft mailing list are public. We are also registered in the AMBER and CCL mailing lists, and we will answer to the queries about the q4md force field tools in these two mailing lists as well. If you have any suggestions about the R.E.D. III.x tools or if you find a bug, send us an e-mail at contact]![q4md-forcefieldtools.org. regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ From owner-chemistry@ccl.net Wed Jul 7 11:14:00 2010 From: "Latchmi Cindy Singh latchmi.singh*gmail.com" To: CCL Subject: CCL: MMFF calculations - help troubleshooting Message-Id: <-42254-100707110630-27325-6wKlPeCehOBljORFADvong===server.ccl.net> X-Original-From: "Latchmi Cindy Singh" Date: Wed, 7 Jul 2010 11:06:28 -0400 Sent to CCL by: "Latchmi Cindy Singh" [latchmi.singh-$-gmail.com] I am running a MMFF calculation to determine the equilibrium conformer. This calculation has been running for 6 days now and is as yet not completed. I know QM calculations are costly, but can molecular mechanics calculations also take this long? Or have I done something wrong? I am using Spartan '08. The molecule that i'm investigating has more than 15 single bonds. I entered the keyword 'SEARCHMETHOD=SPARSE' in the options dialogue for analysis of more conformers. Please advise! Latchmi Singh latchmi.singh__gmail.com 1 Dry River Trace, St. Augustine, Trinidad From owner-chemistry@ccl.net Wed Jul 7 11:49:00 2010 From: "Phil Hasnip pjh503]^[york.ac.uk" To: CCL Subject: CCL: [CCL]: Needs your kind help.. Message-Id: <-42255-100706154539-28646-7PsYfBPBEsHUvUKgHqKZRw(!)server.ccl.net> X-Original-From: Phil Hasnip Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 06 Jul 2010 20:45:27 +0100 Mime-Version: 1.0 Sent to CCL by: Phil Hasnip [pjh503[*]york.ac.uk] On Jun 30 2010, rocky walden rocky.walden19||gmail.com wrote: > Can any one kindly list the protocols needed for MD simulation.. >I wanted to look my protein and ligand changing the conformation after >simulation in a water box. I'm not quite sure what you mean by "protocols", and this is a very broad question, but the basic problems you need to address in molecular dynamics simulations are: a) how to compute the forces on the atoms Unless it's a pretty small protein, density functional theory is going to be impracticable - however there are force-field approximations that may be accurate enough for your purposes. What did you use for your simulations so far? Remember that you're going to want several thousand force-evaluations at the very least if you're going to do molecular dynamics simulations. b) how to integrate the equations of motion In other words once I know the forces, how do I go from the positions and velocities at time t to computing the positions and velocities at time t+dt? Most decent simulation programs will already have a reasonable solution to this - it's common to use the velocity-Verlet algorithm. c) which thermodynamic ensemble is appropriate What is conserved in your simulation - energy or temperature? Volume or pressure? Depending on your answer, you may need to choose an appropriate thermostat and/or barostat. You might even want to worry about whether you should conserve the number of particles or the chemical potential... d) how much time do you need to simulate the system for This depends on what you're actually wanting to see. What are the characteristic time scales for the changes you want to observe? How long will it take for your system to reach thermodynamic equilibrium? e) how large a time step you can use (and still get decent results) The larger the time step ("dt") the quicker your computer simulation will run, but of course the results will be less accurate than using a small dt. These are just a few of the things you would need to consider. There are lots of papers and books on the subject, but personally I'd recommend the book "Understanding Molecular Simulation" by Daan Frenkel and Berend Smit. I've also found "Computer Simulation of Liquids" by Mike Allen and Dominic Tildesley helpful. Yours, Phil Hasnip ------------------------------------------------------- Dr Phil Hasnip Email: pjh503|a|york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 434624 York YO10 5DD From owner-chemistry@ccl.net Wed Jul 7 12:23:00 2010 From: "Emran Heshmati heshmaty||yahoo.com" To: CCL Subject: CCL:G: Molecular electrostatic potential and NBO Message-Id: <-42256-100707111515-8581-nDXR3C1IR8e46YpYpRaNqg_-_server.ccl.net> X-Original-From: Emran Heshmati Content-Type: multipart/alternative; boundary="0-970394246-1278515709=:55753" Date: Wed, 7 Jul 2010 08:15:09 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Emran Heshmati [heshmaty _ yahoo.com] --0-970394246-1278515709=:55753 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Tamer it is very simple by gaussian. just write "pop=3Dnbo" in the rute section. = for example:=20 b3lyp/6-31+g* opt pop=3Dnbo =A0 Best Regards Emran Heshmati P Save a tree... please don't print this e-mail unless you really need to --- On Mon, 5/7/10, tamer sabry El-shazly t_sabry2005~!~hotmail.com wrote: > From: tamer sabry El-shazly t_sabry2005~!~hotmail.com Subject: CCL:G: Molecular electrostatic potential and NBO To: "Heshmati, Emran " Date: Monday, 5 July, 2010, 7:48 PM Sent to CCL by: "tamer sabry El-shazly" [t_sabry2005|,|hotmail.com] dear all an urgent help needed, 1- to provide me by the method of how to obtain or calculate the Molecular = electrostatic potential to evaluate the charge density distributions , is i= t possible using Gaussian only? or extra program needed ( please to recomme= nd this program name if it's necessary to use it in addition to gaussian) 2- How can i perform the natural bond orbital analysis (NBO)=A0=20 your urgent reply will be appreciated in order to finalize a critical issue regards tamer sabry el-shazly +20121526076 t_sabry2005-*-hotmail.com -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-970394246-1278515709=:55753 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Tamer
it is very simple by gaussian. just write "pop=3Dnbo" in the rute sect= ion. for example:
b3lyp/6-31+g* opt pop=3Dnbo

&nb= sp;
Best Regards
Emran = Heshmati
P Save a tree... please don't print this e-mail unless y= ou really need to


--- On Mon, 5/7/10, tamer sab= ry El-shazly t_sabry2005~!~hotmail.com <owner-chemistry/./ccl.net> wrote:

From: tamer sabry El-shazly t_sabry2005~!~hotmail= .com <owner-chemistry/./ccl.net>
Subject: CCL:G: Molecular electrost= atic potential and NBO
To: "Heshmati, Emran " <heshmaty/./yahoo= .com>
Date: Monday, 5 July, 2010, 7:48 PM


Sent to CCL by: "tamer sabry El-shazly" [t_sabry= 2005|,|hotmail.com]

dear all
an urgent help needed,
1- to prov= ide me by the method of how to obtain or calculate the Molecular electrosta= tic potential to evaluate the charge density distributions , is it possible= using Gaussian only? or extra program needed ( please to recommend this pr= ogram name if it's necessary to use it in addition to gaussian)
2- How c= an i perform the natural bond orbital analysis (NBO) 

your urg= ent reply will be appreciated in order to finalize a critical issue
rega= rds
tamer sabry el-shazly
+20121526076
t_sabry2005-*-hotmail.com


-=3D This is automatically added to each message by the maili= ng script =3D-
To recover the email address of the author of the message= , please change
the strange characters on the top line to the /./ sign. Yo= u can also
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--0-970394246-1278515709=:55753-- From owner-chemistry@ccl.net Wed Jul 7 12:58:00 2010 From: "James Eilers jeilers a siue.edu" To: CCL Subject: CCL: MMFF calculations - help troubleshooting Message-Id: <-42257-100707123559-29345-hnR6G9kgjLoPyytDwVW8Og\a/server.ccl.net> X-Original-From: James Eilers Content-Type: multipart/alternative; boundary=Apple-Mail-2--434398959 Date: Wed, 7 Jul 2010 11:35:11 -0500 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: James Eilers [jeilers|*|siue.edu] --Apple-Mail-2--434398959 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed If you are looking at 30 deg increments for 15 bonds, thats 12**15 conformations to evaluate; and that will take a lot of time. This is why the monte-carlo method was invented! On Jul 7, 2010, at 10:06 AM, Latchmi Cindy Singh latchmi.singh*gmail.com wrote: > > Sent to CCL by: "Latchmi Cindy Singh" [latchmi.singh-$-gmail.com] > I am running a MMFF calculation to determine the equilibrium > conformer. This calculation has been running for 6 days now and is as > yet not completed. I know QM calculations are costly, but can > molecular mechanics calculations also take this long? Or have I done > something wrong? > > I am using Spartan '08. The molecule that i'm investigating has more > than 15 single bonds. I entered the keyword 'SEARCHMETHOD=SPARSE' in > the options dialogue for analysis of more conformers. > > Please advise! > > > > Latchmi Singh > latchmi.singh:_:gmail.com > 1 Dry River Trace, St. Augustine, Trinidad> To recover the email address of the author of the message, please > change> > > James E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 --Apple-Mail-2--434398959 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII If you are looking at 30 deg increments for 15 bonds, thats 12**15 conformations to evaluate; and that will take a lot of time. This is why the monte-carlo method was invented! On Jul 7, 2010, at 10:06 AM, Latchmi Cindy Singh latchmi.singh*gmail.com wrote: Sent to CCL by: "Latchmi Cindy Singh" [latchmi.singh-$-gmail.com] I am running a MMFF calculation to determine the equilibrium conformer. This calculation has been running for 6 days now and is as yet not completed. I know QM calculations are costly, but can molecular mechanics calculations also take this long? Or have I done something wrong? I am using Spartan '08. The molecule that i'm investigating has more than 15 single bonds. I entered the keyword 'SEARCHMETHOD=SPARSE' in the options dialogue for analysis of more conformers. Please advise! Latchmi Singh latchmi.singh:_:gmail.com 1 Dry River Trace, St. Augustine, Trinidadhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtHelveticaJames E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 --Apple-Mail-2--434398959-- From owner-chemistry@ccl.net Wed Jul 7 13:33:01 2010 From: "ABHISHEK SHAHI shahi.abhishek1984%%gmail.com" To: CCL Subject: CCL: FREQUENCY Calculation Problem Message-Id: <-42258-100707132044-28830-jAN2YyW/jwbElE5wp+Bmjg^-^server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=000e0cd2e0545f74b7048acf6362 Date: Wed, 7 Jul 2010 22:50:36 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984%gmail.com] --000e0cd2e0545f74b7048acf6362 Content-Type: text/plain; charset=ISO-8859-1 Dear All During frequency calculation (GO3) , my jobs are terminating without error (given below).If i restart the calculation, same or nearly same errors are comming. I don't know that this is memory problem or something else. Thanks a lot . Initially ROUTE :;# MP2=full/aug-cc-PVTZ opt=(maxcycle=100) freq nosymm scf=tight (upto here , optimization has been done but frequency calculation failed ) Restart route section ::# MP2=full/aug-cc-PVTZ opt=(maxcycle=100) freq=restart nosymm scf=tight ERROR ::: **** Warning!!: The largest alpha MO coefficient is .64315315D+02 **** Warning!!: The largest beta MO coefficient is .66802600D+02 Disk-based method using ON**2 memory for 13 occupieds at a time. Permanent disk used for amplitudes= 13168800 words. Estimated scratch disk usage= 585855268 words. Actual scratch disk usage= 564884772 words. JobTyp=2 Pass 1: I= 1 to 13 NPSUse= 8 ParTrn=T ParDer=T DoDerP=T. (rs|ai) integrals will be sorted in core. Actual scratch disk usage= 564884772 words. JobTyp=3 Pass 1: I= 1 to 12 NPSUse= 8 ParTrn=T ParDer=T DoDerP=T. (rs|ai) integrals will be sorted in core. -- With regards; ABHISHEK SHAHI Ph. D. student Prof. E.Arunan's Group Department of Inorganic and Physical Chemistry IISc bangalore-12 Tel No. 080-2293-2384(lab) Official E-mail: shahi[A]ipc.iisc.ernet.in CC:Mail To shahi.abhishek1984[A]gmail.com --000e0cd2e0545f74b7048acf6362 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All
=A0=A0 During frequency calculation (GO3) , my jobs are ter= minating without error (given below).If i restart the calculation, same or = nearly same errors are comming. I don't know that this is memory proble= m or something else.

Thanks a lot .

Initially ROUTE :;# MP2=3Dfull/aug-cc-PVTZ opt=3D(maxcycle=3D100) freq nosymm scf=3Dtight=A0(upto here , optimization has been done but frequency calculation faile= d )


Restart route section ::# MP2=3Dfull/aug-cc-PVTZ opt=3D(maxcycle=3D100) freq=3Drestart nosymm sc= f=3Dtight


ERROR :::
=A0**** Warning!!: The largest alpha MO coefficient is=A0=A0 .64315315D+02<= br>

=A0**** Warning!!: The largest beta MO coefficient is=A0=A0 .668= 02600D+02

=A0Disk-based method using ON**2 memory for 13 occupieds a= t a time.
=A0Permanent disk used for amplitudes=3D=A0=A0=A0 13168800 words.
=A0Est= imated scratch disk usage=3D=A0=A0 585855268 words.
=A0Actual=A0=A0=A0 s= cratch disk usage=3D=A0=A0 564884772 words.
=A0JobTyp=3D2 Pass=A0 1:=A0 = I=3D=A0=A0 1 to=A0 13 NPSUse=3D=A0 8 ParTrn=3DT ParDer=3DT DoDerP=3DT.
=A0(rs|ai) integrals will be sorted in core.
=A0Actual=A0=A0=A0 scratch = disk usage=3D=A0=A0 564884772 words.
=A0JobTyp=3D3 Pass=A0 1:=A0 I=3D=A0= =A0 1 to=A0 12 NPSUse=3D=A0 8 ParTrn=3DT ParDer=3DT DoDerP=3DT.
=A0(rs|a= i) integrals will be sorted in core.



=A0


--
With regards;
=A0ABHISH= EK SHAHI
=A0Ph. D. student
=A0Prof. E.Arunan's Group
=A0De= partment of Inorganic and Physical Chemistry
=A0IISc bangalore-12
= =A0Tel No. =A0 080-2293-2384(lab)
=A0Official E-mail: shahi[A]ipc.i= isc.ernet.in
=A0CC:Mail To =A0shahi.abhishek1984[A]gmail.com
--000e0cd2e0545f74b7048acf6362-- From owner-chemistry@ccl.net Wed Jul 7 15:26:01 2010 From: "Ol Ga eurisco1{}pochta.ru" To: CCL Subject: CCL: FREQUENCY Calculation Problem Message-Id: <-42259-100707152436-19305-e94WndGG63mAcFPUSiJphg^^^server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 7 Jul 2010 15:24:35 -0400 Sent to CCL by: "Ol Ga" [eurisco1,,pochta.ru] Dear ABHISHEK SHAHI, The error message is quite easy to interpret: actual (564884772 words ) scratch space is smaller than estimated (564884772 words) . Possible more than 5 Gb is required for RWF and SCR files to perform such calculation. Sincerely, Ol Ga ---------------------------------- > From: ABHISHEK SHAHI shahi.abhishek1984%%gmail.com Sent: Wednesday, July 07, 2010 9:20 PM To: Ga, Ol Subject: CCL: FREQUENCY Calculation Problem Dear All During frequency calculation (GO3) , my jobs are terminating without error (given below).If i restart the calculation, same or nearly same errors are comming. I don't know that this is memory problem or something else. Thanks a lot . Initially ROUTE :;# MP2=full/aug-cc-PVTZ opt=(maxcycle=100) freq nosymm scf=tight (upto here , optimization has been done but frequency calculation failed ) Restart route section ::# MP2=full/aug-cc-PVTZ opt=(maxcycle=100) freq=restart nosymm scf=tight ERROR ::: **** Warning!!: The largest alpha MO coefficient is .64315315D+02 **** Warning!!: The largest beta MO coefficient is .66802600D+02 Disk-based method using ON**2 memory for 13 occupieds at a time. Permanent disk used for amplitudes= 13168800 words. Estimated scratch disk usage= 585855268 words. Actual scratch disk usage= 564884772 words. JobTyp=2 Pass 1: I= 1 to 13 NPSUse= 8 ParTrn=T ParDer=T DoDerP=T. (rs|ai) integrals will be sorted in core. Actual scratch disk usage= 564884772 words. JobTyp=3 Pass 1: I= 1 to 12 NPSUse= 8 ParTrn=T ParDer=T DoDerP=T. (rs|ai) integrals will be sorted in core. -- With regards; ABHISHEK SHAHI Ph. D. student Prof. E.Arunan's Group Department of Inorganic and Physical Chemistry IISc bangalore-12 Tel No. 080-2293-2384(lab) Official E-mail: shahi|-|ipc.iisc.ernet.in CC:Mail To shahi.abhishek1984|-|gmail.com