From owner-chemistry@ccl.net Sun Sep 16 10:31:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas{:}chem.elte.hu" To: CCL Subject: CCL:G: Geomview Message-Id: <-35162-070916100348-9785-vcTZEDKhWLqd55fr9YW1UQ#server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 16 Sep 2007 15:29:00 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas]*[chem.elte.hu] Hi Tom, Check your version of Gaussian. I tried your input (# was added to the command line, %rwf, %mem %nproc was removed to use the local defaults) with the latest, G03 Rel. D01 and it seems to be fine, it produces the GEOMVIEW input. Best wishes, Ödön On Sat, 2007-09-15 at 11:00 -0400, Tom de Greef t.f.a.d.greef..tue.nl wrote: > Sent to CCL by: "Tom de Greef" [t.f.a.d.greef[#]tue.nl] > Dear all, > I am new relatively new to the field of comp. chemestry. I want to use the program geomview to visualise the solvent cavity as created by the PCM model. It should result in a file which I can open using the Geomview software. However, I have tried several input lines to let Gaussian make the file. I have used the following input line: > %chk=cisamineTDDFTPCM.chk > %mem=1024MB > %nproc=1 > %rwf=z,2000MB,y,2000MB,t,2000MB,u,2000MB,v,2000MB,r,2000MB > b3lyp/6-311+g(d,p) scrf=(pcm,read,solvent=chloroform) > > CisAmine > > 0 1 > O 12.92110000 7.25760000 19.82850000 > O 8.38320000 8.01440000 19.60130000 > O 2.45790000 7.33120000 14.39380000 > O 5.26930000 6.38830000 17.92100000 > N 7.86850000 7.19620000 16.75470000 > H 7.47620000 7.17490000 17.53890000 > N 10.66290000 7.78690000 20.06620000 > N 3.55880000 6.71520000 16.35900000 > C 9.24140000 6.98150000 16.77500000 > C 9.96560000 6.46710000 15.67710000 > H 9.50270000 6.24750000 14.87640000 > C 11.33850000 6.27620000 15.74260000 > H 11.79950000 5.96380000 14.97300000 > C 12.06040000 6.53260000 16.91360000 > H 13.00070000 6.40110000 16.95830000 > C 11.34120000 6.98490000 17.99780000 > C 9.96810000 7.21280000 17.94110000 > C 11.80720000 7.33320000 19.36860000 > C 9.50890000 7.71570000 19.25490000 > C 10.68650000 8.19820000 21.43690000 > C 11.67450000 9.06850000 21.87090000 > H 12.31850000 9.40350000 21.25750000 > C 11.71760000 9.44880000 23.20560000 > H 12.39150000 10.04860000 23.50530000 > C 10.78130000 8.95660000 24.10200000 > H 10.81580000 9.21840000 25.01440000 > C 9.79820000 8.08620000 23.66900000 > H 9.15920000 7.74910000 24.28710000 > C 9.74100000 7.70300000 22.33280000 > H 9.06290000 7.10910000 22.03300000 > C 7.08340000 7.45010000 15.64340000 > C 7.58010000 7.97410000 14.42840000 > H 8.50810000 8.16160000 14.34500000 > C 6.73720000 8.21860000 13.35710000 > H 7.10950000 8.54410000 12.54610000 > C 5.36000000 8.00300000 13.42630000 > H 4.78940000 8.17470000 12.68630000 > C 4.87210000 7.52750000 14.62680000 > C 5.70520000 7.24990000 15.70560000 > C 3.47630000 7.20800000 15.03660000 > C 4.89270000 6.73630000 16.81900000 > C 2.42550000 6.32110000 17.14560000 > C 1.42100000 5.55340000 16.56500000 > H 1.49030000 5.27920000 15.65790000 > C 0.31780000 5.19210000 17.32500000 > H -0.37300000 4.67140000 16.93280000 > C 0.21400000 5.58200000 18.64950000 > H -0.54700000 5.33550000 19.16140000 > C 1.22780000 6.33380000 19.22420000 > H 1.16390000 6.59200000 20.13730000 > C 2.33780000 6.71420000 18.47540000 > H 3.02720000 7.23560000 18.86930000 > > GEOMVIEW > > > > However, this results in the following error: > > Using the following non-standard input for PCM: > GEOMVIEW > End of line while reading PCM input. > Error termination via Lnk1e in /usr/opt/gaussian/g03/l301.exe > > Can someone help me with this problem?? > > Best regards, > > Tom> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Sun Sep 16 12:04:00 2007 From: "Kalyan chaitanya kalyanpulipaka%x%gmail.com" To: CCL Subject: CCL: query reg. docking followed by Dynamics Message-Id: <-35163-070916120223-21647-dXCND8SpYMbDF50o93RD2w(a)server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_3386_575116.1189958535414" Date: Sun, 16 Sep 2007 21:32:15 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka*gmail.com] ------=_Part_3386_575116.1189958535414 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I have a doubt, I am now working on Docking and i learnt that M.Dynamics and simulations would be very useful and efficient way of understanding how exactly two molecules are interacting with each other, i have GROMACS, TINKER and NAMD for the same purpose, but can you tell me- 1. Is it that we can see ligand and receptor coming together and trying to fit with different conformations and finally binding itself with a stable conformation. 2.can any one refer any publication papers who have done Docking followed by Dynamics and simulations in showing the interactions. 3. how relaiable is M.Dynamics and simulations. Thanks in advance, Regards, P.Kalyan ------=_Part_3386_575116.1189958535414 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Hi all,

I have a doubt, I am now working on Docking and i learnt that M.Dynamics and simulations would be very useful and efficient way of understanding how exactly two molecules are interacting with each other, i have GROMACS, TINKER and NAMD for the same purpose, but can you tell me-

1. Is it that we can see ligand and receptor coming together and trying to fit with different conformations and finally binding itself with a stable conformation.

2.can any one refer any publication papers who have done Docking followed by Dynamics and simulations in showing the interactions.

3. how relaiable is M.Dynamics and simulations.

Thanks in advance,

Regards,

P.Kalyan

------=_Part_3386_575116.1189958535414-- From owner-chemistry@ccl.net Sun Sep 16 14:11:00 2007 From: "Frank Neese neese%a%thch.uni-bonn.de" To: CCL Subject: CCL: Orbitals/cube/Mac OS X Message-Id: <-35164-070916130804-17786-h+Qq0spj//HnsoJ5P2AkOQ : server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Sun, 16 Sep 2007 18:07:43 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Frank Neese [neese .. thch.uni-bonn.de] Dear CCL'ers, i would greatly appreciate pointers to appropriate (preferably free) software that allows visualization of molecules structures *and* orbitals/densities on Mac OS X versions 10.4 and higher. The input data may either be cube files or provided by appropriate interfaces. So far, all of my (limited) attempts have failed - there are many nice molecule viewers around but so far i have not found a program that is easy to use and nicely visualizes cube format data. If somebody knows a nice program that accepts the same data in another well documented format - please let me know as well. All the best and many thanks in advance, Frank From owner-chemistry@ccl.net Sun Sep 16 16:00:00 2007 From: "Jerome Kieffer jerome.Kieffer . terre-adelie.org" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35165-070916155507-1636-SUS4YwTzjYDAT42n+ksySQ() server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Sun, 16 Sep 2007 21:54:39 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer^terre-adelie.org] Dear CCLers, I am wondering if any of yours has a piece of software to convert a molecule represented as it's SMILES string into a ".skc" isis draw file. The best would be an open-source code so that I could re-use it but if it is =ABjust=BB free, it is OK for me. Best regards. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ? From owner-chemistry@ccl.net Sun Sep 16 19:12:01 2007 From: "Wolf-D. Ihlenfeldt wdi*o*xemistry.com" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35166-070916190749-8369-hCtCYJtpARj6C3rljWVD0g{:}server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 16 Sep 2007 23:32:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi..xemistry.com] Jerome, that is definitely not a trivial problem, since it involves 2D structure layout and handling a complex binary file format. We are not talking = about a "piece" of software, but thousands (more tens of thousands) of lines of code. You can do this easily with the CACTVS toolkit, but that is not open = source code. You are very welcome to use the free academic scripting = environment to address this task for academic projects. However, commercial or government use, or the use as a link library, requires a license. As far as I know, none of the other converters can *write* skc (or tgf, = the verbose textual variant). Please contact me in case this is still of interest to you. W. D. Ihlenfeldt Xemistry GmbH wdi%xemistry.com --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany Ust.-Id. No. DE 184/93908 : HR Marburg B4713 : EU Ust-Id. No. DE21531632 = : DUNS 34-400-1719=20 > -----Original Message----- > From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net]=20 > Sent: Sunday, September 16, 2007 3:55 PM > To: Ihlenfeldt, W.d. > Subject: CCL: Smiles -> Isis draw >=20 >=20 > Sent to CCL by: Jerome Kieffer=20 > [jerome.Kieffer^terre-adelie.org] Dear CCLers, >=20 > I am wondering if any of yours has a piece of software to=20 > convert a molecule represented as it's SMILES string into a=20 > ".skc" isis draw file. The best would be an open-source code=20 > so that I could re-use it but if it is =ABjust=BB free, it is OK for = me. >=20 > Best regards. > -- > J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre=20 > une rue =E0 contre-sens est moins dangeureux que prendre un=20 > boulevard dans le sens l=E9gal. =C0 qui la faute ? >=20 >=20 >=20 > -=3Dhis is automatically added to each message by the mailing script = =3D > To recover the email address of the author of the message,=20 > please change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl,=20 > Password: search) >=20>=20>=20 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ >=20 >=20 >=20 >=20 From owner-chemistry@ccl.net Sun Sep 16 23:19:00 2007 From: "Vlad vvv900:+:anusf.anu.edu.au" To: CCL Subject: CCL:G: Orbitals/cube/Mac OS X Message-Id: <-35167-070916231508-27463-s6+p1fC1wbMPMvr+t8SAow(!)server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Mon, 17 Sep 2007 12:12:42 +1000 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900,,anusf.anu.edu.au] Dear Frank, > i would greatly appreciate pointers to appropriate (preferably free) > software that allows visualization of molecules structures *and* > orbitals/densities on Mac OS X versions 10.4 and higher. The input data > may either be cube files or provided by appropriate interfaces. You might want to have a look at the JMolEditor (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html) which supports Gaussian input and output files as well as cube files. Several tutorials on how to use JMolEditor with Gaussian are here: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/index.html Best wishes, Vlad -- =============================== Dr. Vladislav Vassiliev Supercomputer Facility, ANU Canberra, ACT, 0200, Australia Phone: +61 2 6125-9694 Fax: +61 2 6125-8199