From owner-chemistry@ccl.net Fri Oct 19 09:13:00 2007 From: "may abdelghani may01dz/a\yahoo.fr" To: CCL Subject: CCL: RE : CCL: a small imaginarily frequency Message-Id: <-35420-071019073411-460-vtWbBYciVCbXBg/QELHZqA-,-server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1040383757-1192790298=:46617" Date: Fri, 19 Oct 2007 12:38:18 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz:-:yahoo.fr] --0-1040383757-1192790298=:46617 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit good morning sir, A " 20i imaginary frequency mode using BP86", sir, you can send me the publication of this information (or send me the reference}, thnak you vey much. "luca bertini luca.bertini(0)unimib.it" a écrit : Sent to CCL by: "luca bertini" [luca.bertini##unimib.it] Dear Nuno, I think that your guideline for the imaginary normal model frequencies does not take into account the fact that rotations (when not sterically hindered) are characterize by low imaginary frequencies, and that in general B3LYP frequencies could be higher in frequency that those computed using GGA BP86, for example. I think that the real problem is how correct is the topology of the DFT PES, compared to that obtained at correlated level. In my experience I have seen real rotation TS with 20i imaginary frequency mode using BP86 (real means that the structure of the TS calculated likely correspond to that of the experiments, with computed barrier in agreement with the experiments like dynamical NMR). So, for me if the TS structure is reasonable, a imaginary frequency of 57i is enough to claim that on the DFT PES, this structure is really a TS. Finally, I'm very curious about the “minimum” with DFT frequency of 300i. Could you send me the reference? ciao, Luca On Mon, 08 Oct 2007 13:23:10 +0100 "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" wrote: > > Sent to CCL by: "Nuno A. G. Bandeira" >[nuno.bandeira|a|ist.utl.pt] > may abdelghani may01dz|*|yahoo.fr wrote: >> Sent to CCL by: "may abdelghani" [may01dz-x-yahoo.fr] >> dear CCLers >> A unique imaginarily frequency of -57 cm-1 is enough to >>say, that the >> corresponding structure is a transition states and not >>another local >> minima? The task was be a transition states search. > > If it's not a weak interaction you're dealing with then >I'd say it's a minimum. Just so you know there have been >"minima" reported in the literature with as much as -300 >cm-1. > > But the usual arbitrary guideline is discard imaginary >frequencies between 0 and -100 cm-1. They generally can >be put off as computational error within DFT. > > > -- > Nuno A. G. Bandeira, AMRSC > Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, >Faculty of Science > University of Lisbon - C8 building, Campo Grande, > 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html > Doctoral student .. IST,Lisbon > -- > > > > -= 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> > E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net or >useConferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, >Password: search)> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-1040383757-1192790298=:46617 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
good morning sir,
A " 20i  imaginary frequency mode using BP86", sir, you can send me the publication of this information (or send me the reference}, thnak you vey much. 
 
"luca bertini luca.bertini(0)unimib.it" <owner-chemistry++ccl.net> a écrit :

Sent to CCL by: "luca bertini" [luca.bertini##unimib.it]

Dear Nuno,

I think that your guideline for the imaginary normal model
frequencies does not take into account the fact that
rotations (when not sterically hindered) are characterize
by
low imaginary frequencies, and that in general B3LYP
frequencies could be higher in frequency that those
computed using GGA BP86, for example.

I think that the real problem is how correct is the
topology of the DFT PES, compared to that obtained at
correlated level.

In my experience I have seen real rotation TS with 20i
imaginary frequency mode using BP86 (real means that the
structure of the TS calculated likely correspond to
that of the experiments, with computed barrier in
agreement with the experiments like dynamical NMR).

So, for me if the TS structure is reasonable, a imaginary
frequency of 57i is enough to claim that on the DFT PES,
this structure is really a TS.

Finally, I'm very curious about the “minimum” with DFT
frequency of 300i. Could you send me the reference?

ciao, Luca


On Mon, 08 Oct 2007 13:23:10 +0100
"Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt"
wrote:
>
> Sent to CCL by: "Nuno A. G. Bandeira"
>[nuno.bandeira|a|ist.utl.pt]
> may abdelghani may01dz|*|yahoo.fr wrote:
>> Sent to CCL by: "may abdelghani" [may01dz-x-yahoo.fr]
>> dear CCLers
>> A unique imaginarily frequency of -57 cm-1 is enough to
>>say, that the
>> corresponding structure is a transition states and not
>>another local
>> minima? The task was be a transition states search.
>
> If it's not a weak interaction you're dealing with then
>I'd say it's a minimum. Just so you know there have been
>"minima" reported in the literature with as much as -300
>cm-1.
>
> But the usual arbitrary guideline is discard imaginary
>frequencies between 0 and -100 cm-1. They generally can
>be put off as computational error within DFT.
>
>
> --
> Nuno A. G. Bandeira, AMRSC
> Graduate researcher and molecular sculptor
> Inorganic and Theoretical Chemistry Group,
>Faculty of Science
> University of Lisbon - C8 building, Campo Grande,
> 1749-016 Lisbon,Portugal
> http://cqb.fc.ul.pt/intheochem/nuno.html
> Doctoral student .. IST,Lisbon
> --
>
>
>
> -= 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>
> E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net or
>useConferences:
>http://server.ccl.net/chemistry/announcements/conferences/
>
> Search Messages: http://www.ccl.net/htdig (login: ccl,
>Password: search)>
> RTFI:
>http://www.ccl.net/chemistry/aboutccl/instructions/>
>
>


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Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-1040383757-1192790298=:46617-- From owner-chemistry@ccl.net Fri Oct 19 09:48:01 2007 From: "soumya s soumya_samineni:-:rediffmail.com" To: CCL Subject: CCL: g98:CIS Message-Id: <-35421-071019051832-21315-OKi/gbJOmUpIL7Hhac9T7A!A!server.ccl.net> X-Original-From: "soumya s" Date: Fri, 19 Oct 2007 05:18:28 -0400 Sent to CCL by: "soumya s" [soumya_samineni---rediffmail.com] hi all Where can i find some information "on how to analyse the CIS calculation output ?" thanx in advance soumya From owner-chemistry@ccl.net Fri Oct 19 10:33:01 2007 From: "soumya s soumya_samineni+*+rediffmail.com" To: CCL Subject: CCL: g98:Maximum number of allowed steps Message-Id: <-35422-071019102733-23410-NoAsCqW8t55DWgUTMe1OYg]~[server.ccl.net> X-Original-From: "soumya s" Date: Fri, 19 Oct 2007 10:27:28 -0400 Sent to CCL by: "soumya s" [soumya_samineni-.-rediffmail.com] hi all Is there no way of increasing the MAXIMUM allowed number of steps for an optimisation ? thanx in advance and more thanx for the way the CCL subscribers r helping me to learn more soumya From owner-chemistry@ccl.net Fri Oct 19 12:26:01 2007 From: "Close, David M. CLOSED^mail.etsu.edu" To: CCL Subject: CCL:G: g98:Maximum number of allowed steps Message-Id: <-35423-071019122310-20443-XnKohn8YlVvx9BI8GNcv6g-*-server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Fri, 19 Oct 2007 12:22:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED=-=mail.etsu.edu] That's easy. The Gaussian manual says to use MaxCycle=3DN. There are of course two cycles in an iteration. Each SCF iteration takes a number of cycles, and the optimization requires a number of steps. You can increase both of these if necessary. -----Original Message----- > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net]=20 Sent: Friday, October 19, 2007 10:27 AM To: Close, David M. Subject: CCL: g98:Maximum number of allowed steps Sent to CCL by: "soumya s" [soumya_samineni-.-rediffmail.com] hi all Is there no way of increasing the MAXIMUM allowed number of steps for an optimisation ? thanx in advance and more thanx for the way the CCL subscribers r helping me to learn more soumya -=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 Fri Oct 19 13:01:00 2007 From: "Tamas Gunda tgunda1 : puma.unideb.hu" To: CCL Subject: CCL: Input file for STERIMOL program Message-Id: <-35424-071019050153-19615-eNfTnMjv7ml13FVR/qESnA^_^server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Fri, 19 Oct 2007 10:03:20 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda1/a\puma.unideb.hu] I have the documentation somewhere, but I need time to find it... However, try to use the program Mol2mol to calculate the sterimol parameters. It uses the original algorythm and accepts a lot of common input formats. http://web.interware.hu/frenzy/mol2mol/ Tamas Gunda = = = = = = = = = = = = Prof. Tamas E. Gunda University of Debrecen Department of Pharmaceutical Chemistry H-4010 Debrecen, POB 36, Hungary tgunda2 {at} puma.unideb.hu ----- Original Message ----- > From: "Jinsong Zhao jszhao:+:mail.hzau.edu.cn" To: "Gunda, Tamas E " Sent: Thursday, October 18, 2007 14:40 PM Subject: CCL: Input file for STERIMOL program > > Sent to CCL by: "Jinsong Zhao" [jszhao-#-mail.hzau.edu.cn] > Dear all, > > Recently, I hope to use STERIMOL program (QCPE: QCMP093) to calculate some > Verloop's parameters. However, I don't know how to prepare a input file > for this program. Although I have some example input files, I don't > understand those code. > > I have searched google, and don't find any information about the rules to > write a input file for STERIMOL. > > > If you happen to have any manual or hints or experience on it, please give > me a hand. > > Thanks in advance! > > Best regards, > > Jinsong Zhao > > -- > Jinsong Zhao, Dr. > College of Resources and Environment, > Huazhong Agricultural University, > Wuhan 430070, P. R. China > E-mail: jszhao ~ mail.hzau.edu.cn> > > From owner-chemistry@ccl.net Fri Oct 19 16:59:00 2007 From: "David Gallagher gallagher.da++gmail.com" To: CCL Subject: CCL: Large Computation Time Leap in Mopac and A Question About pm6 Message-Id: <-35425-071019152209-26471-YYZYwnxo6fxpKDVP9okNcQ^_^server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 19 Oct 2007 11:17:28 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da[A]gmail.com] One possible reason for running very slowly in previous versions of MOPAC2007, is using the default RHF for a metal containing compound with an odd number of electrons. If it is supposed to be a radical, then you should try UHF for these situations. The latest version of MOPAC2007 can automatically adjust the settings for metal containing compounds with an odd number of electrons. If this is not the issue, then if you send me the molecule file, I would be happy to take a closer look. Regards, David Gallagher CAChe Research At 12:15 AM 10/15/2007, Sina T reli sinatureli:_:gmail.com wrote: >Sent to CCL by: "Sina T reli" [sinatureli!^!gmail.com] > >- I am using mopac2007 to do some geometry optimizations with mndod >and pm6. My first subject was a molecule of size 141 which was >handled quite nicely and fast and ended about in 30 minutes. However >when I added a ligand that was about of 20 atoms in size, the >calculation time leaped to like 2 days. The cycles werent even >initiated before half a day passed... I used .mopac as the first >output file and when I wanted to optimized the ligated one I used >.xyz format with some atoms fixed to their coordinates. Is there >something I am doing wrong or is this leap expected? And also I read >that mopac 2007 isnt very practical for molecules of size above 600. >Say if I use it for a molecule of size 400 atoms would it take too >long on a 3.8 ghz 1gb ram machine? (I might plan to continue the >work in a advanced computational center then...) > >Thanks From owner-chemistry@ccl.net Fri Oct 19 20:12:00 2007 From: "Yasset Perez Riverol yasset.perez-x-biocomp.cigb.edu.cu" To: CCL Subject: CCL: about program for molecular descriptor Message-Id: <-35426-071019151417-25576-zzDIj9zYjFmIxcV1uY6b2Q*server.ccl.net> X-Original-From: Yasset Perez Riverol Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Fri, 19 Oct 2007 14:33:11 -0400 MIME-Version: 1.0 Sent to CCL by: Yasset Perez Riverol [yasset.perez{:}biocomp.cigb.edu.cu] Hi: Does anybody know a "free" library or package to compute molecular descriptors, beside CDK API, or a free program. Any advise will be apperiated))!!! =2D-=20 Ing. Yasset P=C3=A9rez Riverol. Bioinformatic. Group CIGB, La Habana, Cuba. From owner-chemistry@ccl.net Fri Oct 19 22:31:01 2007 From: "Gonzalo Jim nez-Os s gjimenez,,unizar.es" To: CCL Subject: CCL: Parallel runs in Turbomole Message-Id: <-35427-071019222727-31816-3lcwTsk9ZS9FXuq0eQasGg**server.ccl.net> X-Original-From: "Gonzalo Jim nez-Os s" Date: Fri, 19 Oct 2007 22:27:23 -0400 Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez[-]unizar.es] Dear CCL'ers In the last days I've doing some benchmarking with Turbomole, and I am experiencing some kind of trouble when submitting parallel jobs. Whereas the serial jobs run in a really straightforward and quick fashion, every parallel run crashes at its first calculation stages. I do believe that I have set up the parallel environment correctly by following the manual guidelines: export PARA_ARCH=MPI export PATH=TURBODIR/bin/sysname:PATH export PARNODES=2 My sysname seems to be OK (em64t-unknown-linux-gnu_mpi), but when I launch the executable (e.g. jobex -ri) the calculation crashes after entering my ssh password. Here is the output: ***************************** convgrep will be taken out of the TURBODIR directory Password: /opt/soft/tmoleX/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/ridft_mpi: error while loading shared libraries: libguide.so: cannot open shared object file: No such file or directory /opt/soft/tmoleX/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/ridft_mpi: error while loading shared libraries: libguide.so: cannot open shared object file: No such file or directory MPI Application rank 0 exited before MPI_Init() with status 127 OPTIMIZATION CYCLE 1 Password: /opt/soft/tmoleX/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/rdgrad_mpi: error while loading shared libraries: libguide.so: cannot open shared object file: No such file or directory MPI Application rank 0 exited before MPI_Init() with status 127 relax ended abnormally program stopped. relax ended abnormally program stopped. run relax for a cartesian step relax ended abnormally program stopped. ERROR: Module relax failed to run properly - please check output job.1 and job.last for the reason ***************************** It seems like it does not find de shared libraries that I have located in TURBODIR/libso/em64t-unknown-linux-gnu_mpi. It is a bit confusing to me... Any idea about that? I am currently using Intel EM64T Dual Core processors. On the other hand, do you know about any benchmark results centered on the scaling ability of Turbomole? Regards, Gonzalo