Dr Gilles Frapper Groupe de Chimie Quantique Appliquée LACCO UMR 6503 CNRS - Université de Poitiers 40 av.recteur Pineau 86022 Poitiers Cedex tél : +33 (0)5 49 45 35 74 - fax : +33 (0) 5 49 45 34 99 http://yargla.labo.univ-poitiers.fr / gilles.frapper*univ-poitiers.fr

------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget**ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------

Sent to CCL by: "Henry Martinez" [hmartine:_:gmail.com] Hello everyone, This is the first time I need to restart a Freq calculation (I need some thermochemistry data) and I am using this input ONLY %chk=n9.chk %nproc=2 %mem=120MW # freq=Restart b3lyp/6-311+g(3df,2p) However the calculation started and finished in "Normal termination" in less than 20 sec, without any Thermochemistry data, obviously that is not what I want. Can anybody tell what am I doing wrong and how can I fixed. Thanks you very much for your help.E-mail to subscribers: CHEMISTRY**ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

with everything else and ***.cub in the end.<= /div>

And this is the ending of my output:

Evaluate density.

Using the spin density.

Map the density over a grid of points, CutOff=3D= 1.00D-06

Writing cube to file ***.cub.

IGUnit=3D -31 Origin=3D -6.040794 -5.152992 -3.6= 95616

N1=3D 72 XYZInc=3D 0.176392 0.000000 0.000000

N2=3D 61 XYZInc=3D 0.000000 0.176392 0.000000

N3=3D 42 XYZInc=3D 0.000000 0.000000 0.176392

I am pretty sure that it's not due to time r= unning out and it just comes to a abrupt stop. I just wonder if anyone has = the similar experience=A0on this and a=A0solution=A0at hand. Thank you very= =A0much!

Jane=A0

--90e6ba47682b3316cf049b3c6734-- From owner-chemistry@ccl.net Tue Feb 1 13:43:00 2011 From: "Hanneke Jansen johanna.jansen_._novartis.com" To: CCL Subject: CCL: Launching COMP Together Message-Id: <-43823-110201131129-7512-08vpNhgOvpTe2hB913LMaw:-:server.ccl.net> X-Original-From: "Hanneke Jansen" Date: Tue, 1 Feb 2011 13:11:28 -0500 Sent to CCL by: "Hanneke Jansen" [johanna.jansen*|*novartis.com] Dear Colleagues, The Computers in Chemistry (COMP) Division of the ACS is excited to launch a new initiative, COMP Together ! The COMP Together initiative includes tools and a network of local champions to facilitate COMP members getting together on a local and informal level (seminars, networking events, mentoring lunches). The COMP Together tools are hosted on the COMP website and will support regular/recurring events as well as ad-hoc events. We invite you to register for COMP Together through this link: http://www.acscomp.org/COMP_Together/reg_form.php Registration for a certain local area will add your email address to the announcements of COMP Together events happening in that area. You are then also able to register for an event and indicate any special requirements with that RSVP. Local champions have been identified for a number of areas, but on the registration page we are also asking if you are wiling to volunteer for this or if youre available to assist the champions. The local champions are the ones who set up the events and monitor RSVPs, all through the COMP Together tools. They would coordinate with presenters, scout for locations and possibly engage sponsors. Our goal is to have several champions in each area, so you can share the work. The tools on the website should make the operational details of sending invites and managing RSVPs very easy. If you are interested in learning more about the local champion role, you can email johanna.jansen---novartis.com We look forward to your participation in this new initiative and hope that this will strengthen our scientific community. Best regards, The COMP Together team San Francisco Bay Area: Hanneke Jansen, Vickie Tsui, Siegfried Leung San Diego: Patrick Lee, Sara Nichols, Rommie Amaro Northern New Jersey: Ed Sherer, Chris Harwell New York City: Chris Harwell Southern New Jersey/PA: Neysa Nevins, Chuck Reynolds, Kate Holloway Boston: Melissa Landon, Michelle Lamb, Ken Mattes, Lee Herman Washington DC/VA: Samual Toba, Noel Southall RTP: Rachelle Bienstock Connecticut: Veer Shanmugasundaram From owner-chemistry@ccl.net Tue Feb 1 14:18:00 2011 From: "Edroaldo Lummertz da Rocha edroaldo*o*gmail.com" To: CCL Subject: CCL: Building Nanoparticles Message-Id: <-43824-110201110206-8953-G2a39anfKjDUeqjnOtizCQ a server.ccl.net> X-Original-From: "Edroaldo Lummertz da Rocha" Date: Tue, 1 Feb 2011 11:02:05 -0500 Sent to CCL by: "Edroaldo Lummertz da Rocha" [edroaldo:_:gmail.com] Hi, I am starting to construct models to use in molecular dynamics simulations and I can not find information about how build atomistic nanoparticles and nanomaterials models. For example, I need to model a truncated octahedron gold nanoparticle. What is the methodology for that? I build the FCC unit cell and the periodic structure but I do not know how to get a spherical morphology, for example. Could anyone give me a direction to do that? Is there a free software? I read some previous messages here and I found a post about Materials Studio. However I do not have access to Materials Studio and I need free software or some methodology for that. Any direction is useful. Thanks so much. Edroaldo Lummertz da Rocha edroaldo-.-gmail.com From owner-chemistry@ccl.net Tue Feb 1 16:00:00 2011 From: "dhacademic dhacademic]=[gmail.com" To: CCL Subject: CCL: PMF problem Message-Id: <-43825-110201155721-22935-H8zwSEHiorl8bVIFdA2/7Q- -server.ccl.net> X-Original-From: dhacademic Content-Type: multipart/alternative; boundary=20cf30433f12361f2f049b3ec620 Date: Tue, 1 Feb 2011 15:57:02 -0500 MIME-Version: 1.0 Sent to CCL by: dhacademic [dhacademic|*|gmail.com] --20cf30433f12361f2f049b3ec620 Content-Type: text/plain; charset=ISO-8859-1 Hi everyone, I have a problem in 2D PMF calculations. There are two reaction coordinates (RC) in my system. RC1 stands for conformational change of protein (saying RC1 ranges from 1 to 10, where RC1=1 means closed state of protein, RC1=10 means open state), and RC2 is the distance between ligand and active site (RC2 ranges from 1 to 10, where RC2=1 means ligand bound state, RC2=10 means ligand escaped state). After the time-consuming umbrella sampling calculations (with amber9) on two RCs, the 2D free energy profile can be obtained with WHAM program. However, the open state of protein with ligand bound to active site (RC1=10, RC2=1) is found to be a minimum on the free energy surface, while the closed state with ligand bound has higher energy (RC1=1, RC2=1). This is opposite to what I have expected, where the closed state of protein with ligand bound should be a stable state. Then the umbrella sampling data of different RC1 (from 1 to 10) with fixed RC2 (RC2=1) are used to get quasi-1D free energy profile of protein conformational change with ligand bound, and the results seem to be reasonable: the open state is energetic unfavorable, and the closed state has a minimum. The system stability in quasi-1D free energy profile is reasonable. Besides, umbrella sampling on RC1 (no bias potential is imposed on RC2, and the ligand position and orientation is almost unchanged because there are lots of favorable interactions between ligand and active site is strong) was done on the same system. The generated 1D-PMF results is quite similar to the quasi-1D one, and quite different to the 2D-PMF results when RC2=1. All the structures as well as the data have been carefully checked. Everything looks good, but the results look strange. I do not understand why the stability of the system in 2D-PMF and quasi-1D-PMF is different. As the results from 2D-PMF are inconsistent with common knowledge of protein-ligand complex, I think there may be something wrong with my 2D-PMF calculations. Can anyone give some suggestions? Thanks in advance! Best, Hao --20cf30433f12361f2f049b3ec620 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi everyone,

I have a problem in 2D PMF calc= ulations.

=A0

There are two reaction coordina= tes (RC) in my system. RC1 stands for conformational change of protein (saying RC1 rang= es > from 1 to 10, where RC1=3D1 means closed state of protein, RC1=3D10 means o= pen state), and RC2 is the distance between ligand and active site (RC2 ranges = > from 1 to 10, where RC2=3D1 means ligand bound state, RC2=3D10 means ligand esca= ped state). After the time-consuming umbrella sampling calculations (with amber= 9) on two RCs, the 2D free energy profile can be obtained with WHAM program. However, the open state of protein with ligand bound to active site (RC1=3D= 10, RC2=3D1) is found to be a minimum on the free energy surface, while the closed state with ligand bound has higher energy (RC1=3D1, RC2=3D1). This is opposite to= what I have expected, where the closed state of protein with ligand bound should b= e a stable state.

=A0

Then the umbrella sampling data= of different RC1 (from 1 to 10) with fixed RC2 (RC2=3D1) are used to get quasi-1D free e= nergy profile of protein conformational change with ligand bound, and the results seem to= be reasonable: the open state is energetic unfavorable, and the closed state h= as a minimum. The system stability in quasi-1D free energy profile is reasonable= .

=A0

Besides, umbrella sampling on R= C1 (no bias potential is imposed on RC2, and the ligand position and orientation is alm= ost unchanged because there are lots of favorable interactions between ligand a= nd active site is strong) was done on the same system. The generated 1D-PMF re= sults is quite similar to the quasi-1D one, and quite different to the 2D-PMF res= ults when RC2=3D1.

=A0

All the structures as well as t= he data have been carefully checked. Everything looks good, but the results look strange= . I do not understand why the stability of the system in 2D-PMF and quasi-1D-PM= F is different. As the results from 2D-PMF are inconsistent with common knowledg= e of protein-ligand complex, I think there may be something wrong with my 2D-PMF calculations. Can anyone give some suggestions? Thanks in advance!

=A0

Best,

Hao

--20cf30433f12361f2f049b3ec620-- From owner-chemistry@ccl.net Tue Feb 1 16:35:00 2011 From: "Cheri McFerrin cmcfer1^-^tigers.lsu.edu" To: CCL Subject: CCL:G: Cannot generate a .cub file with G03 Message-Id: <-43826-110201142915-17930-WFClny3615vpaWI5NX71kg+/-server.ccl.net> X-Original-From: Cheri McFerrin Content-Type: multipart/alternative; boundary=0016e644c58c1d62f7049b3d8b4e Date: Tue, 1 Feb 2011 13:28:56 -0600 MIME-Version: 1.0 Sent to CCL by: Cheri McFerrin [cmcfer1:_:tigers.lsu.edu] --0016e644c58c1d62f7049b3d8b4e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable hi jane: here is what i would do. run a single point energy using qcisd(full)/6-31g*. afterwards, run this command in order to convert your .chk file to a .fchk file formchk file.chk file.fchk next, run this command to generate a .cube file cubegen 0 density=3Dscf file.fchk 0 h more, on formchk and cubegen and be found at gaussian.com >>keywords>>gaussian09utilities the cubegen and formchk utilities will be the same for G03. hope this helps!! cheri 2011/2/1 =E6=AE=B7=E5=81=A5 janeyin600|*|gmail.com > Hello there, > > I am trying to generate a cube file with Gaussian03. However, every time = it > stops at a certain place. My command line is : > *# QCISD(full)/6-31G* density=3Dcurrent cube=3D(spin,coarse)* > with everything else and ***.cub in the end. > > And this is the ending of my output: > > Evaluate density. > > Using the spin density. > > Map the density over a grid of points, CutOff=3D 1.00D-06 > > Writing cube to file ***.cub. > > IGUnit=3D -31 Origin=3D -6.040794 -5.152992 -3.695616 > > N1=3D 72 XYZInc=3D 0.176392 0.000000 0.000000 > > N2=3D 61 XYZInc=3D 0.000000 0.176392 0.000000 > > N3=3D 42 XYZInc=3D 0.000000 0.000000 0.176392 > > I am pretty sure that it's not due to time running out and it just comes = to > a abrupt stop. I just wonder if anyone has the similar experience on this > and a solution at hand. Thank you very much! > > Jane > --0016e644c58c1d62f7049b3d8b4e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable hi jane:

here is what i would do. =C2=A0run a single poi= nt energy using qcisd(full)/6-31g*.

afterwards, ru= n this command in order to convert your .chk file to a .fchk file