From owner-chemistry@ccl.net Thu Apr 17 01:26:00 2014 From: "Matthias Heger mheger^_^gwdg.de" To: CCL Subject: CCL: Wrong symmetry Message-Id: <-49934-140417012118-19939-iiLpZ8r0CjdRxh8jsZ+tTg * server.ccl.net> X-Original-From: Matthias Heger Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="----YQ3TZ7J9IGN39QLH5Q6KEWJ71W573T" Date: Thu, 17 Apr 2014 07:20:54 +0200 MIME-Version: 1.0 Sent to CCL by: Matthias Heger [mheger()gwdg.de] ------YQ3TZ7J9IGN39QLH5Q6KEWJ71W573T Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Dear Reza, it could be instructive to look at the vibrational mode which is associated with the imaginary frequency (that's what it actually is, the minus sign is just a label). Your system has not reached a minimum of the potential energy in some coordinates, and you can tell by the vibration "where it wants to go". This may happen, as Thomas mentioned, with undue symmetry constraints. Best -M. On 17. April 2014 01:39:40 MESZ, "Reza Shojaei shojaei81**gmail.com" wrote: > >Sent to CCL by: "Reza Shojaei" [shojaei81:-:gmail.com] >Dear All, > >I have optimized Aniline (C6H5NH2) using different methods and basis >sets, and despite Aniline is a single conformer compound but my >optimization falls on a transition state with negative frequency. > >What does it mean? Does Aniline have another conformer?!! > >How can I solve this problem in G09? It must have no negative >frequency.>To recover the email address of the author of the message, please >change------YQ3TZ7J9IGN39QLH5Q6KEWJ71W573T Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit Dear Reza,

it could be instructive to look at the vibrational mode which is associated with the imaginary frequency (that's what it actually is, the minus sign is just a label). Your system has not reached a minimum of the potential energy in some coordinates, and you can tell by the vibration "where it wants to go". This may happen, as Thomas mentioned, with undue symmetry constraints.

Best
-M.

On 17. April 2014 01:39:40 MESZ, "Reza Shojaei shojaei81**gmail.com" <owner-chemistry]_[ccl.net> wrote:

Sent to CCL by: "Reza  Shojaei" [shojaei81:-:gmail.com]
Dear All,

I have optimized Aniline (C6H5NH2) using different methods and basis sets, and despite Aniline is a single conformer compound but my optimization falls on a transition state with negative frequency. 

What does it mean? Does Aniline have another conformer?!!

How can I solve this problem in G09? It must have no negative frequency.




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------YQ3TZ7J9IGN39QLH5Q6KEWJ71W573T-- From owner-chemistry@ccl.net Thu Apr 17 12:17:01 2014 From: "Andrew Voronkov drugdesign|yandex.ru" To: CCL Subject: CCL: selectivity evaluation Message-Id: <-49935-140417121535-3688-mruRJteVrKCjzCRLop9k6A^server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 17 Apr 2014 20:15:27 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign_-_yandex.ru] Dear CCL users, I have a task of comparison of a family of the related proteins and analysis of their selectivity. There are three main stages, which I would define for it. Is it possible for you to recommend software and programs, which you consider as the best in the next areas: 1. Tools and software for the analysis of protein surfaces, detection of cavities, grooves and other potential binding sites 2. Tools and software for the evaluation of the druggability of potential binding sites. 3. Some tools and software for the comparison of the potential binding sites, selection of most interesting amino acids which differ etc. Best regards, Andrey From owner-chemistry@ccl.net Thu Apr 17 16:24:01 2014 From: "Jinsong Zhao jszhao^yeah.net" To: CCL Subject: CCL: Mopac6 and Mopac7 code Message-Id: <-49936-140417162224-14645-XUDNBfg6apDXHfCGv+8T4w]_[server.ccl.net> X-Original-From: Jinsong Zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 17 Apr 2014 13:22:13 -0700 MIME-Version: 1.0 Sent to CCL by: Jinsong Zhao [jszhao.:.yeah.net] I have compared the Mopac6 code in CCL archives with that in OpenMopac website. It's obvious the later had been much more revised. For Mopac7 from OpenMopac website, although it also heavily revised compared to that in CCL, it did not include the patches provided in CCL archives, even that for the most obvious bugs. So, I am confused. Best, Jinsong On 2014/4/16 16:12, John McKelvey jmmckel(-)gmail.com wrote: > > I believe that there is a cleaned up version of MOPAC-7 in the CCL > archives. There may also be a copy of MOPAC-6. > > John > > > On Wed, Apr 16, 2014 at 4:23 PM, Jinsong Zhao jszhao]![yeah.net > > wrote: > > > Sent to CCL by: Jinsong Zhao [jszhao]*[yeah.net ] > Hello, > > I just hope to get a credible code, and then read it. So I don't > care about the binary release with plenty of new features. > > Regards, > Jinsong > > On 2014/4/16 0:35, Daniel Jana dfjana,,gmail.com > wrote: > > > Sent to CCL by: Daniel Jana [dfjana**gmail.com ] > Hello, > > The author of Mopac does not make immediately clear on the website > which subversion you are downloading. The file is updated when a new > version comes out, but the name stays the same. As such, downloads > done in different moments may end up being different patch levels of > Mopac. > > But I agree with Mark, why not do things properly and download > it from > the website? It's free and you are sure you download the latest > version of the program (and with no malware attached). > > Best, > Daniel > > On 16 April 2014 01:38, Jinsong Zhao jszhao/ayeah.net > > > wrote: > > > Sent to CCL by: Jinsong Zhao [jszhao++yeah.net > ] > Hi there, > > I have googled and found that there are various copy of > Mopac6 and Mopac7 > code with different patch level. However, the reliability > can not be > justified. Thus, I am wondering whether there is a copy of > Mopac6 and/or > Mopac7 that are considered as credible by you, the > computational chemist. > Thank you very much for any hints. > > Best wishes, > Jinsong > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel++gmail.com From owner-chemistry@ccl.net Thu Apr 17 16:58:01 2014 From: "Vel Murugan murugan4chemistry*gmail.com" To: CCL Subject: CCL:G: Wrong symmetry Message-Id: <-49937-140417164901-25177-M+yFSxZT+S8BcEcrsGC8IQ ~~ server.ccl.net> X-Original-From: Vel Murugan Content-Type: multipart/alternative; boundary=001a1134aa0e4e7b9e04f74329c8 Date: Fri, 18 Apr 2014 02:18:34 +0530 MIME-Version: 1.0 Sent to CCL by: Vel Murugan [murugan4chemistry[]gmail.com] --001a1134aa0e4e7b9e04f74329c8 Content-Type: text/plain; charset=UTF-8 Dear Reza, For a minimum energy geometry you should find all positive frequencies. Furthermore my guess would be that all the frequencies should come the same as with an exact calculation (i.e. rotational and translational modes drop, modes across the minimum of a well should have positive frequencies and modes across a maximum imaginary frequencies). If it is more than either the structure you found isn't what you where looking for either the integration was to inaccurate and you should retry the calculation at a higher precision. If you using Gaussian software? you always get the output corresponding to a geometry optimization step, with four criteria that have to be fulfilled. If all of them say "YES", you're OK... For a minimum geometry, all remaining vibrations should be positive. If some are close to zero, you may have free rotations in your molecule. If any of them are below, say, 30-50 cm-1, you should treat thermodynamic contributions with caution, because the harmonic approximation is no longer valid. In your case try to look at the geometry for the corresponding negative frequency and start the new calculation from that structure. I hope this will help you. With Best Regards, Velmurugan G On Thu, Apr 17, 2014 at 10:50 AM, Matthias Heger mheger^_^gwdg.de < owner-chemistry=-=ccl.net> wrote: > Dear Reza, > > it could be instructive to look at the vibrational mode which is > associated with the imaginary frequency (that's what it actually is, the > minus sign is just a label). Your system has not reached a minimum of the > potential energy in some coordinates, and you can tell by the vibration > "where it wants to go". This may happen, as Thomas mentioned, with undue > symmetry constraints. > > Best > -M. > > On 17. April 2014 01:39:40 MESZ, "Reza Shojaei shojaei81**gmail.com" > wrote: > > > >Sent to CCL by: "Reza Shojaei" [shojaei81:-:gmail.com] > >Dear All, > > > >I have optimized Aniline (C6H5NH2) using different methods and basis > >sets, and despite Aniline is a single conformer compound but my > >optimization falls on a transition state with negative frequency. > > > >What does it mean? Does Aniline have another conformer?!! > > > >How can I solve this problem in G09? It must have no negative > >frequency.>To recover the email address of the author of the message, > please > >change------YQ3TZ7J9IGN39QLH5Q6KEWJ71W573T > Content-Type: text/html; charset="utf-8" > Content-Transfer-Encoding: 8bit > > Dear Reza,
>
> it could be instructive to look at the vibrational mode which is > associated with the imaginary frequency (that's what it actually is, > the minus sign is just a label). Your system has not reached a minimum of > the potential energy in some coordinates, and you can tell by the vibration > "where it wants to go". This may happen, as Thomas mentioned, > with undue symmetry constraints.
>
> Best
> -M.

On 17. April 2014 01:39:40 MESZ, > "Reza Shojaei shojaei81**gmail.com" > <owner-chemistry{=}ccl.net> wrote:
style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, > 204); padding-left: 1ex;"> > 

Sent to CCL by: "Reza  Shojaei" [shojaei81:-: href="http://gmail.com">gmail.com]
Dear All,

I have
> optimized Aniline (C6H5NH2) using different methods and basis sets, and
> despite Aniline is a single conformer compound but my optimization falls on
> a transition state with negative frequency. 

What does it mean?
> Does Aniline have another conformer?!!

How can I solve this
> problem in G09? It must have no negative frequency.



 /

      


>  


>  

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 />
-- *VELMURUGAN G* --001a1134aa0e4e7b9e04f74329c8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Reza,

=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= For a minimum energy geometry you should find all positive frequencies. Furthermore my guess would be that all the=C2=A0 <= /span>frequencies should come the same as with an exact calculation (i.e. rotational and translational modes drop, modes acro= ss the minimum of a well should have positive frequencies and modes across a maximum imaginary frequencies). If it is more than either the= =C2=A0 structure you found isn't what you where looking for either the integration was to inaccurate and you should retry t= he calculation at a higher precision.

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 If you using Gaussian software?=C2=A0 you always get the output corresponding to a geometry optimization step, with four criteria that have= to be fulfilled.=C2=A0 If all of them say "YES", you're OK... For a minimum geometry, all remaining vibrations should be positive.=C2=A0 If some are close to=C2=A0 <= /span>zero, you=C2=A0 may have free rotations in your molecule.=C2=A0 I= f any of them are below, say, 30-50 cm-1, you should treat thermodynamic contributions with caution, because the harm= onic approximation is no longer valid. In your case try to look at the geometry = for the corresponding negative frequency and start the new calculation from tha= t structure. I hope this will help you.


With Best Regards,


Velmurugan G





On Thu, Apr 1= 7, 2014 at 10:50 AM, Matthias Heger mheger^_^gwd= g.de <owner-chemistry=-=ccl.net> wrote:
Dear Reza,

it could be instructive to look at the vibrational mode which is associated= with the imaginary frequency (that's what it actually is, the minus si= gn is just a label). Your system has not reached a minimum of the potential= energy in some coordinates, and you can tell by the vibration "where = it wants to go". This may happen, as Thomas mentioned, with undue symm= etry constraints.

Best
-M.

On 17. April 2014 01:39:40 MESZ, "Reza Shojaei shojaei81**gmail.com" <owner-chemistry{= =3D}ccl.net> wrote:
>
>Sent to CCL by: "Reza =C2=A0Shojaei" [shojaei81:-:gmail.com]
>Dear All,
>
>I have optimized Aniline (C6H5NH2) using different methods and basis >sets, and despite Aniline is a single conformer compound but my
>optimization falls on a transition state with negative frequency.
>
>What does it mean? Does Aniline have another conformer?!!
>
>How can I solve this problem in G09? It must have no negative
>frequency.>To recover the email address of the author of the m= essage, please
>change------YQ3TZ7J9IGN39QLH5Q6KEWJ71W573T
Content-Type: text/html; charset=3D"utf-8"
Content-Transfer-Encoding: 8bit

<html><head></head><body>Dear Reza, <br>
<br>
it could be instructive to look at the vibrational mode which is associated= with the imaginary frequency (that&#39;s what it actually is, the minu= s sign is just a label). Your system has not reached a minimum of the poten= tial energy in some coordinates, and you can tell by the vibration &quo= t;where it wants to go&quot;. This may happen, as Thomas mentioned, wit= h undue symmetry constraints. <br>
<br>
Best<br>
-M. <br><br><div class=3D"gmail_quote">On 17. A= pril 2014 01:39:40 MESZ, &quot;Reza Shojaei shojaei81**<a href=3D&qu= ot;http://gmail.com"= ;>gmail.com</a>= &quot; &lt;owner-chemistry{=3D}ccl.net&gt; wrote:<blockquote class=3D"gmail_quote= " style=3D"margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(= 204, 204, 204); padding-left: 1ex;">
<pre class=3D"k9mail"><br />Sent to CCL by: "Rez= a =C2=A0Shojaei" [shojaei81:-:<a href=3D"http://gmail.com">gmail.com</a>]<br />Dear All,&l= t;br /><br />I have optimized Aniline (C6H5NH2) using different me= thods and basis sets, and despite Aniline is a single conformer compound bu= t my optimization falls on a transition state with negative frequency. <= br /><br />What does it mean? Does Aniline have another conformer?= !!<br /><br />How can I solve this problem in G09? It must have= no negative frequency.<br /><br /><br /><br /<br /= <br /<br /<br /><br /<br /> =C2=A0 =C2=A0 =C2=A0<a = href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"&g= t;http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br /&= gt;<br /<br /> =C2=A0 =C2=A0 =C2=A0<a href=3D"http://ww= w.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/c= gi-bin/ccl/send_ccl_message</a><br /><br /<br /> = =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/chemistry/sub_uns= ub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</= a><br /><br />Before posting, check wait time at: <a href= =3D"http://www.cc!
=C2=A0l.net">http://www.ccl.net</a>&= lt;br /><br />Job: <a href=3D"http://www.ccl.net/jobs">http://www.ccl.net/jobs</a= > <br />Conferences: <a href=3D"http://server= .ccl.net/chemistry/announcements/conferences">http= ://server.ccl.net/chemistry/announcements/conferences</a>/<br = /><br />Search Messages: <a href=3D"http://www.ccl.n= et/chemistry/searchccl/index.shtml">http://www.ccl.net/ch= emistry/searchccl/index.shtml</a><br /><br /<br />= =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/spammers.txt">http://www.ccl.n= et/spammers.txt</a><br /><br />RTFI: <a
href=3D"http://www.ccl.net/chemistry/aboutccl/instructions&q= uot;>http://www.ccl.net/chemistry/aboutccl/instructions</a&= gt;/<br /><br /><br /></pre></blockquote><= /div></body></html>



--

VELMURUGAN G
--001a1134aa0e4e7b9e04f74329c8-- From owner-chemistry@ccl.net Thu Apr 17 17:53:00 2014 From: "Andreas Goetz agoetz+*+sdsc.edu" To: CCL Subject: CCL: AMBER workshop announcement Message-Id: <-49938-140417173833-28564-Sge8/9VnJh/tw35LDCb/OQ|server.ccl.net> X-Original-From: "Andreas Goetz" Date: Thu, 17 Apr 2014 17:38:31 -0400 Sent to CCL by: "Andreas Goetz" [agoetz(a)sdsc.edu] Dear all, We are glad to announce the Amber Workshop 2014 that will be held in Barcelona from the 2nd to 6th June at the Vertex Building (UPC Campus). The course will be taught by Ross C. Walker and Adrian E. Roitberg and will be hosted by the IRB Barcelona and the Barcelona Supercomputing Center. More info: http://mmb.pcb.ub.es/www/amber2014 Please feel free to forward this announcement to all your contacts. With the best regards, The Organizing Team * Program The duration of the meeting is 5 days, from 2nd of June to 6th. Typically there will be lectures 3 hours per day, and hands-on tutorials, about 5 hours per day. The content of the Workshop will include: * Molecular Dynamics with Amber * Using VMD to visualize AMBER * Dealing with non-standard residues * Building protein-ligand complexes * Statistical Mechanics for Free Energy Calculations * MM/PBSA calculations * Calculating relative binding free energies for protein/carbohydrate complexes * Enhanced sampling techniques * Maximizing Performance (Parallel Execution and NVIDIA GPU Acceleration) * Umbrella sampling simulations * Analyzing Simulations * Introduction to QM/MM Calculations * Lipid Simulations with AMBER The target audience is graduate students and postdocs as well as a few faculty interested in learning about Molecular Dynamics techniques. The course is designed to introduce Molecular Dynamics techniques from an introductory perspective but will progress quickly. Some experience with the Linux operating system is essential but experience with AMBER or other molecular dynamics packages is not required. * Registration The number is limited to 40. Given the limited number of seats you will be requested to fill a pre- registration form. Fill the pre-registration form at: http://mmb.pcb.ub.es/www/amber2014 Important: Pre-registration deadline is 28 of April. Organizers will review applications and invite those selected to register by May 8th. From 8th of May, if there are seats available, the organizers will accept further applications. Registration fees are 190 euros. Attendees are expected to bring their own laptop. The organization will provide a pendrive with all necessary software and training material. Lunch and coffee breaks are included.