From owner-chemistry@ccl.net Fri Nov 2 00:34:01 2007 From: "Mohana Sundharam Velayutham info_-_pharmolae.com" To: CCL Subject: CCL: Requesting software Message-Id: <-35549-071101083245-12582-ntk3ZLaJCaLFDVX5zajMBA[#]server.ccl.net> X-Original-From: "Mohana Sundharam Velayutham" Date: Thu, 1 Nov 2007 08:32:39 -0400 Sent to CCL by: "Mohana Sundharam Velayutham" [info[A]pharmolae.com] Dear Concerned, My name is Mohan. I'm novice in this field and i've list of chemicals in a SDF file. I want freeware application which could calculate the Lipinski Parameters for the chemicals in the SDF file. Please guide me where i can find it. Thanks in advance. My mail ID is info^pharmolae.com Regards, Mohan From owner-chemistry@ccl.net Fri Nov 2 01:18:01 2007 From: "jitrayut jitonnom jitrayut.018-,-gmail.com" To: CCL Subject: CCL: Out of disk space Message-Id: <-35550-071102005751-9789-F5DxofajEjGzAi8JTnEpcw/a\server.ccl.net> X-Original-From: "jitrayut jitonnom" Content-Type: multipart/alternative; boundary="----=_Part_16023_33513495.1193975555509" Date: Fri, 2 Nov 2007 10:52:35 +0700 MIME-Version: 1.0 Sent to CCL by: "jitrayut jitonnom" [jitrayut.018.{=}.gmail.com] ------=_Part_16023_33513495.1193975555509 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCl users, I am facing a problem about CIS optimization. The error here make me confuses because i try to increase the split file to more than 200GB and MAXDISK=500GB but why the error occur ? So, any suggestion would be great. Here is the end of output: Semi-Direct transformation. ModeAB= 4 MOrb= 141 LenV= 262007968 LASXX= 5075604354 LTotXX= 5075604354 LenRXX= 10227944433 LTotAB= 5152340079 MaxLAS= 4000375296 LenRXY= 0 NonZer= 15303548787 LenScr= 30627856384 LnRSAI= 4000375296 LnScr1= 8009023488 LExtra= 28876389 Total= 52894075990 MaxDsk= 67108864000 SrtSym= T ITran= 3 No file to extend for IUnit= 1 -- out of disk space. Error termination in NtrErr: NtrErr called from NtrExt. Also, the heading of input: %nprocl=6 Will use up to 6 processors via Linda. %nprocs=2 Will use up to 2 processors via shared memory. %mem=2GB %rwf=a1,20GB,a2,20GB,a3,20GB,a4,20GB,a5,20GB,a6,20GB,a7,20GB,a8,20GB,a9,20GB,b1, 20GB,b2,20GB,b3,20GB,b4,20GB,b5,20GB,b6,20GB,b7,20GB,b8,20GB,b9,20GB %nosave -------------------------------------------- #p RCIS(Root=1)/3-21G MaxDisk=500GB Opt Test -------------------------------------------- 1/18=20,38=1/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=5,11=1,16=1,25=1,30=1/1,2,8,3; 4/7=1/1; 5/5=2,38=5/2; 8/6=1,10=1,27=67108864000/1,4; 9/8=1,15=1,27=67108864000,42=3/14; 10/5=4/2; 6/7=2,8=2,9=2,10=2/1; 7/12=6,13=5,14=1/1,2,3,16; 1/18=20/3(3); 2/9=110/2; 6/7=2,8=2,9=2,10=2/1; 99//99; 2/9=110/2; 3/5=5,11=1,16=1,25=1,30=1/1,2,8,3; 4/5=5,7=1,16=3/1; 5/5=2,38=5/2; 8/6=1,10=1,27=67108864000/1,4; 9/8=1,15=1,27=67108864000,42=3,49=4/14; 10/5=4/2; 7/12=6,13=5,14=1/1,2,3,16; 1/18=20/3(-8); 2/9=110/2; 6/7=2,8=2,9=2,10=2/1; 99//99; Leave Link 1 at Wed Oct 31 15:27:23 2007, MaxMem= 268435456 cpu: 13.2 Thanks in advance, Jitrayut Jitonnom Computational Simulation and Modeling Laboratory (CSML) Chiang Mai University Thailand ------=_Part_16023_33513495.1193975555509 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCl users,
 
I am facing a problem about CIS optimization. The error here make me confuses because i try to increase the split file to more than 200GB and MAXDISK=500GB but why the error occur ?
So, any suggestion would be great.
 
Here is the end of output:
 
 Semi-Direct transformation.
 ModeAB=           4 MOrb=           141 LenV=     262007968
 LASXX=   5075604354 LTotXX=  5075604354 LenRXX= 10227944433
 LTotAB=  5152340079 MaxLAS=  4000375296 LenRXY=           0
 NonZer= 15303548787 LenScr= 30627856384 LnRSAI=  4000375296
 LnScr1=  8009023488 LExtra=    28876389 Total=  52894075990
 MaxDsk= 67108864000 SrtSym=           T ITran=            3
 No file to extend for IUnit=  1 -- out of disk space.
 Error termination in NtrErr:
 NtrErr called from NtrExt.
 
Also, the heading of input:
 
 %nprocl=6
 Will use up to    6 processors via Linda.
 %nprocs=2
 Will use up to    2 processors via shared memory.
 %mem=2GB
 %rwf=a1,20GB,a2,20GB,a3,20GB,a4,20GB,a5,20GB,a6,20GB,a7,20GB,a8,20GB,a9,20GB,b1,
 20GB,b2,20GB,b3,20GB,b4,20GB,b5,20GB,b6,20GB,b7,20GB,b8,20GB,b9,20GB
 %nosave
 --------------------------------------------
 #p RCIS(Root=1)/3-21G MaxDisk=500GB Opt Test
 --------------------------------------------
 1/18=20,38=1/1,3;
 2/9=110,17=6,18=5,40=1/2;
 3/5=5,11=1,16=1,25=1,30=1/1,2,8,3;
 4/7=1/1;
 5/5=2,38=5/2;
 8/6=1,10=1,27=67108864000/1,4;
 9/8=1,15=1,27=67108864000,42=3/14;
 10/5=4/2;
 6/7=2,8=2,9=2,10=2/1;
 7/12=6,13=5,14=1/1,2,3,16;
 1/18=20/3(3);
 2/9=110/2;
 6/7=2,8=2,9=2,10=2/1;
 99//99;
 2/9=110/2;
 3/5=5,11=1,16=1,25=1,30=1/1,2,8,3;
 4/5=5,7=1,16=3/1;
 5/5=2,38=5/2;
 8/6=1,10=1,27=67108864000/1,4;
 9/8=1,15=1,27=67108864000,42=3,49=4/14;
 10/5=4/2;
 7/12=6,13=5,14=1/1,2,3,16;
 1/18=20/3(-8);
 2/9=110/2;
 6/7=2,8=2,9=2,10=2/1;
 99//99;
 Leave Link    1 at Wed Oct 31 15:27:23 2007, MaxMem=  268435456 cpu:      13.2
 
 
Thanks in advance,
 
Jitrayut Jitonnom
Computational Simulation and Modeling Laboratory (CSML)
Chiang Mai University
Thailand
------=_Part_16023_33513495.1193975555509-- From owner-chemistry@ccl.net Fri Nov 2 01:52:00 2007 From: "neeraj Misra neerajmisra\a/hotmail.com" To: CCL Subject: CCL:G: PED CALCULATION Message-Id: <-35551-071102012231-24930-qHW0w21DN6Ce71lc+xnEkw^-^server.ccl.net> X-Original-From: "neeraj Misra" Date: Fri, 2 Nov 2007 01:22:27 -0400 Sent to CCL by: "neeraj Misra" [neerajmisra##hotmail.com] I WOULD BE THANKFUL IF ANYONE OF YOU COULD SUGGEST ME HOW TO CALCULATE THE POTENTIAL ENERGY DISTRIBUTION (PED) FROM A GAUSSIAN OUTPUT.ANY FREE SOFTWARE FOR THIS WOULD BE A BIG HELP. From owner-chemistry@ccl.net Fri Nov 2 06:13:01 2007 From: "marcel.swart{:}icrea.es" To: CCL Subject: CCL: Calculation of Proton Affinity Message-Id: <-35552-071101192458-20646-d13bc3mUg8HuskBwXZnnXQ_+_server.ccl.net> X-Original-From: marcel.swart{:}icrea.es Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 1 Nov 2007 23:22:40 +0100 MIME-Version: 1.0 Sent to CCL by: marcel.swart,,icrea.es And you might also want to have a look at: M. Swart, E. R=F6sler and F.M. Bickelhaupt "Proton Affinities in Water of Maingroup-Element Hydrides. Effects of =20 Hydration and Methyl Substitution" Eur. J. Inorg. Chem. 2007, 3646-3654 M. Swart, E. R=F6sler and F.M. Bickelhaupt "Proton Affinities of Maingroup-Element Hydrides and Noble Gases: =20 Trends Across the Periodic Table, Structural Effects and DFT Validation" J. Comput. Chem. 2006, 27, 1486-1493 M. Swart and F.M. Bickelhaupt "Proton Affinities of Anionic Bases: Trends Across the Periodic Table, =20 Structural Effects, and DFT Validation" J. Chem. Theor. Comp. 2006, 2, 281-287