From owner-chemistry@ccl.net Mon Sep 30 06:52:00 2013
From: "Adrian Stevens adrian.stevens*accelrys.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: Announcing the release of Discovery Studio 4.0
Message-Id: <-49210-130930064937-11528-MFxjwMaRh9khpMkFV4usLw=server.ccl.net>
X-Original-From: "Adrian Stevens" <adrian.stevens-$-accelrys.com>
Date: Mon, 30 Sep 2013 06:49:36 -0400
Sent to CCL by: "Adrian Stevens" [adrian.stevens###accelrys.com]
Accelrys is very pleased to announce the release of the latest version of
Discovery Studio 4.0, our most complete and integrated solution for both
biologics and small molecules-based research. Version 4.0 includes many new
features and enhancements including:
* Simulations sciences
- Faster robust support for ns-scale MD simulations
- Improved simulations workflow
- Faster & robust Explicit solvation builder
- Enhanced Molecular Dynamics analysis tools
* Biologics research
- New! Disulfide bond predictor
- New! Multiple simultaneous mutations
- Updated: Antibody database
(Includes support to add your own antibody structures)
- Updated: Antibody modeling workflows
* Small-molecules drug research
- New! Non-bond interaction monitors
(including the most extensive set of favourable, unfavourable and
unsatisfied interactions)
- Updated In-situ FBDD lead optimization
- Updated In-situ FBDD core-hopping tools
- Updated Find Activity Cliffs using MMPs
* Partner Science
- CHARMm c37b2 (fully integrated charmm36 support)
- NAMD v9.2 (New! NAMD is now included with Discovery Studio!)
- MODELER 9v12
- DMol3 version 6.1 SP2
- VAMP version 10.0
- Updated support for CCDC's GOLD
* Core/Platform
- Significantly improved client memory management
- Supports the latest Accelrys Enterprise Platform release (v9.1)
Learn how to accelerate molecular simulations for your drug discovery
research, with Discovery Studio 4.0! Register now for our live webinar
series at http://accelrys.com/webinars/discovery-studio
From owner-chemistry@ccl.net Mon Sep 30 07:27:00 2013
From: "thomas.bogaerts:ugent.be" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: g09 frequency calculation error
Message-Id: <-49211-130930041347-16028-EfSnuIES4i4+8Elo/U4gZg-#-server.ccl.net>
X-Original-From: <thomas.bogaerts*_*ugent.be>
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Date: Mon, 30 Sep 2013 10:14:15 +0200
MIME-Version: 1.0
Sent to CCL by: [thomas.bogaerts..ugent.be]
Dear Kursad,
g09 uses two different algorithms to do a frequency calculation (solving the
CPHF equations)
The standard one uses a lot of RAM memory but is very fast. However when the
number of CPHF equations exceeds 5000 by default gaussian uses another
algorithm, this tries to save RAM memory by storing intermediate results on
a hard disk. This takes very long making the calculations practically
inactive.
In order to solve this add an extra option: CPHF(MaxInv=10000). This puts
the maximum number of CPHF equations for the basic algorithm to 10000. Make
sure you have enough memory available when doing this.
kind regards
-----Original Message-----
> From: kursad oguz patriscanary.:.gmail.com
Sent: Sunday, September 29, 2013 4:06 AM
To: Bogaerts, Thomas
Subject: CCL:G: g09 frequency calculation error
Sent to CCL by: "kursad oguz" [patriscanary- -gmail.com]
Dear All,
I am doing frequency calculation of some transition metal complex with
gaussian 09 on linux based computer sistem. my all try ended with the same
output. There is no error line end of output file. Please help me.
Thanks in advance...
my output is following.
%nprocshared=16
Will use up to 16 processors via shared memory.
%mem=8GB
%chk=nibar.chk
-------------------------------------------------------
# opt freq ub3lyp/genecp iop(5/10=-1) geom=connectivity
...................
...................
...............
.................
End of G2Drv Frequency-dependent properties file 722 does not exist.
IDoAtm=11111111111111111111111111111111111111111111111111
IDoAtm=11111111111111111111111111111
Differentiating once with respect to electric field.
with respect to dipole field.
Differentiating once with respect to nuclear coordinates.
There are 240 degrees of freedom in the 1st order CPHF.
IDoFFX=5.
240 vectors produced by pass 0 Test12= 3.47D-13 1.00D-09 XBig12=
1.00D+03 6.30D+00.
AX will form 36 AO Fock derivatives at one time.
240 vectors produced by pass 1 Test12= 3.47D-13 1.00D-09 XBig12=
4.46D+02 1.94D+00.
239 vectors produced by pass 2 Test12= 3.47D-13 1.00D-09 XBig12=
4.56D+00 1.58D-01.
237 vectors produced by pass 3 Test12= 3.47D-13 1.00D-09 XBig12= 2.34D-
02 1.32D-02.
................
...................
..................
......................
.....................
20 vectors produced by pass112 Test12= 3.47D-13 1.00D-09 XBig12= 1.66D-
14 2.54D-09.
20 vectors produced by pass113 Test12= 3.47D-13 1.00D-09 XBig12= 2.44D-
14 2.72D-09.
20 vectors produced by pass114 Test12= 3.47D-13 1.00D-09 XBig12= 4.54D-
14 4.87D-09.
20 vectors produced by pass115 Test12= 3.47D-13 1.00D-09 XBig12= 2.16D-
14 2.91D-09.
20 vectors produced by pass116 Test12= 3.47D-13 1.00D-09 XBig12= 2.34D-
14 2.92D-09.
20 vectors produced by pass117 Test12= 3.47D-13 1.00D-09 XBig12= 1.76D-
14 2.50D-09.
20 vectors produced by pass118 Test12= 3.47D-13 1.00D-09 XBig12= 1.93D-
14 2.65D-09.
20 vectors produced by pass119 Test12= 3.47D-13 1.00D-09 XBig12= 1.11D-
14 2.13D-09.
20 vectors produced by pass120 Test12= 3.47D-13 1.00D-09 XBig12= 3.34D-
14 3.87D-09.
19 vectors produced by pass121 Test12= 3.47D-13 1.00D-09 XBig12= 1.04D-
14 2.18D-09.
6 vectors produced by pass122 Test12= 3.47D-13 1.00D-09 XBig12= 4.62D-
15 1.17D-09.
Applied DIIS recursively to reduced A of dimension 6486.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
From owner-chemistry@ccl.net Mon Sep 30 12:21:00 2013
From: "Partha Sengupta anapspsmo-$-gmail.com" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: data below the no of imaginary frequency
Message-Id: <-49212-130929144901-15660-Yjxfoes5uBH5mbqp05xMxg~~server.ccl.net>
X-Original-From: Partha Sengupta <anapspsmo . gmail.com>
Content-Type: multipart/alternative; boundary=047d7b15a779df3b5f04e78a2b1d
Date: Mon, 30 Sep 2013 00:18:54 +0530
MIME-Version: 1.0
Sent to CCL by: Partha Sengupta [anapspsmo++gmail.com]
--047d7b15a779df3b5f04e78a2b1d
Content-Type: text/plain; charset=ISO-8859-1
Hello, All CCL user I am in query for a question. There is a lot of data
after the no of imaginary frequency. as for example given below. What are
these numbers?
Waiting for reply
Partha Sarathi Sengupta
.
NImag=1||0.87194168,0.03973045,0.64341951,0.37602276,-0.01
260824,0.41239695,-0.06250317,0.06427093,-0.05345900,0.57358802,0.0213
3547,-0.03660313,0.01609967,-0.12220700,0.95141832,-0.04949240,0.04047
935,-0.00953025,0.23429484,-0.13017701,0.31918798,-0.30843842,0.044054
42,-0.15109610,0.00258145,0.00028158,-0.00080338,0.31901925,0.04106014
,-0.07435731,0.02525235,-0.00223104,-0.00735956,-0.00040112,-0.0439279
6,0.07549406,-0.15028717,0.02717171,-0.13210777,-0.00062570,0.00115654
,0.00359341,0.16480395,-0.02810712,0.12625839,-0.00004034,0.00518729,-
0.00350309,-0.00013140,-0.00177362,-0.00261743,-0.00030873,-0.00071359
,-0.00022576,0.54842834,0.00641785,-0.00334228,0.00321778,-0.02661088,
-0.00522971,-0.01602228,0.00057823,0.00135019,0.00019260,-0.08051345,0
.64687612,-0.00355124,0.00472570,0.00272673,-0.00121559,-0.00019685,0.
00291987,-0.00063147,-0.00058936,0.00041904,0.06865189,0.01419455,0.57
334103,-0.00109087,0.00075529,-0.00030863,0.00115880,0.00038221,0.0011
8793,-0.00029889,-0.00039296,0.00003977,-0.12702028,0.08012729,-0.0965
4255,0.14616336,-0.00113695,0.00051281,-0.00019052,0.00006617,0.000718
48,0.00034948,-0.00022309,-0.00022865,0.00005127,0.08206266,-0.1517323
2,0.10524336,-0.08459517,0.16181705,-0.00033394,0.00031376,0.00013423,
0.00089668,-0.00003772,0.00108657,-0.00007266,-0.00015467,-0.00002372,
-0.09515618,0.10403416,-0.17998012,0.10307679,-0.11816109,0.19653361,0
.00053068,-0.00163527,0.00032879,-0.00188047,0.00085355,-0.00188881,-0
.00004496,0.00010801,0.00004775,-0.09384254,0.08596263,0.04548539,-0.0
0692128,0.01479793,0.00920115,0.10604703,-0.00052137,-0.00120062,0.000
16693,-0.00115485,0.00080474,-0.00192432,-0.00000052,0.00003664,-0.000
08843,0.08467229,-0.24839748,-0.11117087,0.00657900,-0.01639113,-0.009
86303,-0.08579160,0.27159938,-0.00017758,-0.00120505,0.00018001,-0.000
47697,0.00051416,-0.00049804,-0.00000628,0.00007827,0.00003026,0.04429
235,-0.10669781,-0.11897601,-0.00918402,0.02207772,0.01420610,-0.05386
103,0.11907983,0.13059135,0.00036052,-0.00140715,-0.00035177,0.0006146
1,0.00245255,0.00091145,0.00013393,0.00011049,-0.00007109,-0.10357151,
-0.00163433,0.04317216,0.00863493,0.00444082,-0.01265426,-0.01288879,-
0.00713730,0.01453084,0.51960649,-0.00030034,-0.00098831,-0.00009492,-
0.00154435,0.00096899,0.00006379,0.00000933,0.00001817,0.00002729,0.00
616332,-0.08848254,0.01535041,-0.01894679,-0.00741530,0.01991243,0.018
90122,0.00879749,-0.02186245,-0.08890436,0.66970396,0.00001307,-0.0009
3639,-0.00030256,-0.00081215,-0.00046491,-0.00075749,-0.00002696,-0.00
006059,-0.00015334,0.02160714,0.00971686,-0.13653913,0.02247778,0.0094
1456,-0.02399610,0.01699484,0.00825371,-0.01934643,0.00997200,0.101149
86,0.55367383,-0.00000408,0.00015051,0.00018607,0.00000212,-0.00052926
,-0.00032841,-0.00001562,-0.00000841,0.00000989,-0.01034078,0.01742370
,0.01282086,0.00113676,-0.00046560,-0.00055728,-0.00215487,-0.00207796
,0.00292447,-0.10725818,0.09727289,0.05895985,0.11996473,0.00009066,0.
00019376,0.00005770,0.00025958,-0.00012428,-0.00009326,-0.00000252,-0.
00000898,0.00001093,-0.00712541,0.01228075,0.00745708,0.00056138,0.000
42033,-0.00074541,-0.00229692,-0.00039187,0.00250770,0.09143540,-0.239
61314,-0.11960866,-0.09562252,0.26405480,-0.00017319,-0.00011225,-0.00
015808,0.00000771,0.00030136,0.00025023,-0.00000070,0.00000180,-0.0000
0158,0.01355556,-0.02031823,-0.01330655,-0.00119635,-0.00026816,0.0006
6749,0.00277000,0.00231950,-0.00285273,0.05789757,-0.12467860,-0.13949
268,-0.06073444,0.12981708,0.15183800,-0.00241653,-0.00366378,-0.00116
613,0.00016837,0.00109722,0.00009822,-0.00015892,-0.00005695,-0.000136
87,0.02109821,-0.01736395,0.01944399,-0.00592881,-0.00210692,0.0062065
3,0.00016140,-0.00031015,0.00163526,-0.12224127,0.02923142,-0.01828769
,-0.00706340,0.00792232,-0.01103228,0.40012671,-0.00096104,-0.00060422
,-0.00036248,-0.00093821,-0.00143622,-0.00088626,0.00007269,0.00015152
,0.00006837,-0.00249857,-0.01283405,0.01777286,-0.00009676,0.00026276,
-0.00126723,0.00201492,0.00185551,-0.00529269,0.04481640,-0.12800032,0
......
--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
--047d7b15a779df3b5f04e78a2b1d
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<div dir=3D"ltr"><div><div>Hello, All CCL user I am in query for a question=
. There is a lot of data after the no of imaginary frequency. as for exampl=
e given below. What are these numbers?<br></div>Waiting for reply<br></div>
Partha Sarathi Sengupta<br>=A0. <br><div><div>NImag=3D1||0.87194168,0.03973=
045,0.64341951,0.37602276,-0.01<br>=A0260824,0.41239695,-0.06250317,0.06427=
093,-0.05345900,0.57358802,0.0213<br>=A03547,-0.03660313,0.01609967,-0.1222=
0700,0.95141832,-0.04949240,0.04047<br>
=A0935,-0.00953025,0.23429484,-0.13017701,0.31918798,-0.30843842,0.044054<b=
r>=A042,-0.15109610,0.00258145,0.00028158,-0.00080338,0.31901925,0.04106014=
<br>=A0,-0.07435731,0.02525235,-0.00223104,-0.00735956,-0.00040112,-0.04392=
79<br>
=A06,0.07549406,-0.15028717,0.02717171,-0.13210777,-0.00062570,0.00115654<b=
r>=A0,0.00359341,0.16480395,-0.02810712,0.12625839,-0.00004034,0.00518729,-=
<br>=A00.00350309,-0.00013140,-0.00177362,-0.00261743,-0.00030873,-0.000713=
59<br>
=A0,-0.00022576,0.54842834,0.00641785,-0.00334228,0.00321778,-0.02661088,<b=
r>=A0-0.00522971,-0.01602228,0.00057823,0.00135019,0.00019260,-0.08051345,0=
<br>=A0.64687612,-0.00355124,0.00472570,0.00272673,-0.00121559,-0.00019685,=
0.<br>
=A000291987,-0.00063147,-0.00058936,0.00041904,0.06865189,0.01419455,0.57<b=
r>=A0334103,-0.00109087,0.00075529,-0.00030863,0.00115880,0.00038221,0.0011=
<br>=A08793,-0.00029889,-0.00039296,0.00003977,-0.12702028,0.08012729,-0.09=
65<br>
=A04255,0.14616336,-0.00113695,0.00051281,-0.00019052,0.00006617,0.000718<b=
r>=A048,0.00034948,-0.00022309,-0.00022865,0.00005127,0.08206266,-0.1517323=
<br>=A02,0.10524336,-0.08459517,0.16181705,-0.00033394,0.00031376,0.0001342=
3,<br>
=A00.00089668,-0.00003772,0.00108657,-0.00007266,-0.00015467,-0.00002372,<b=
r>=A0-0.09515618,0.10403416,-0.17998012,0.10307679,-0.11816109,0.19653361,0=
<br>=A0.00053068,-0.00163527,0.00032879,-0.00188047,0.00085355,-0.00188881,=
-0<br>
=A0.00004496,0.00010801,0.00004775,-0.09384254,0.08596263,0.04548539,-0.0<b=
r>=A00692128,0.01479793,0.00920115,0.10604703,-0.00052137,-0.00120062,0.000=
<br>=A016693,-0.00115485,0.00080474,-0.00192432,-0.00000052,0.00003664,-0.0=
00<br>
=A008843,0.08467229,-0.24839748,-0.11117087,0.00657900,-0.01639113,-0.009<b=
r>=A086303,-0.08579160,0.27159938,-0.00017758,-0.00120505,0.00018001,-0.000=
<br>=A047697,0.00051416,-0.00049804,-0.00000628,0.00007827,0.00003026,0.044=
29<br>
=A0235,-0.10669781,-0.11897601,-0.00918402,0.02207772,0.01420610,-0.05386<b=
r>=A0103,0.11907983,0.13059135,0.00036052,-0.00140715,-0.00035177,0.0006146=
<br>=A01,0.00245255,0.00091145,0.00013393,0.00011049,-0.00007109,-0.1035715=
1,<br>
=A0-0.00163433,0.04317216,0.00863493,0.00444082,-0.01265426,-0.01288879,-<b=
r>=A00.00713730,0.01453084,0.51960649,-0.00030034,-0.00098831,-0.00009492,-=
<br>=A00.00154435,0.00096899,0.00006379,0.00000933,0.00001817,0.00002729,0.=
00<br>
=A0616332,-0.08848254,0.01535041,-0.01894679,-0.00741530,0.01991243,0.018<b=
r>=A090122,0.00879749,-0.02186245,-0.08890436,0.66970396,0.00001307,-0.0009=
<br>=A03639,-0.00030256,-0.00081215,-0.00046491,-0.00075749,-0.00002696,-0.=
00<br>
=A0006059,-0.00015334,0.02160714,0.00971686,-0.13653913,0.02247778,0.0094<b=
r>=A01456,-0.02399610,0.01699484,0.00825371,-0.01934643,0.00997200,0.101149=
<br>=A086,0.55367383,-0.00000408,0.00015051,0.00018607,0.00000212,-0.000529=
26<br>
=A0,-0.00032841,-0.00001562,-0.00000841,0.00000989,-0.01034078,0.01742370<b=
r>=A0,0.01282086,0.00113676,-0.00046560,-0.00055728,-0.00215487,-0.00207796=
<br>=A0,0.00292447,-0.10725818,0.09727289,0.05895985,0.11996473,0.00009066,=
0.<br>
=A000019376,0.00005770,0.00025958,-0.00012428,-0.00009326,-0.00000252,-0.<b=
r>=A000000898,0.00001093,-0.00712541,0.01228075,0.00745708,0.00056138,0.000=
<br>=A042033,-0.00074541,-0.00229692,-0.00039187,0.00250770,0.09143540,-0.2=
39<br>
=A061314,-0.11960866,-0.09562252,0.26405480,-0.00017319,-0.00011225,-0.00<b=
r>=A0015808,0.00000771,0.00030136,0.00025023,-0.00000070,0.00000180,-0.0000=
<br>=A00158,0.01355556,-0.02031823,-0.01330655,-0.00119635,-0.00026816,0.00=
06<br>
=A06749,0.00277000,0.00231950,-0.00285273,0.05789757,-0.12467860,-0.13949<b=
r>=A0268,-0.06073444,0.12981708,0.15183800,-0.00241653,-0.00366378,-0.00116=
<br>=A0613,0.00016837,0.00109722,0.00009822,-0.00015892,-0.00005695,-0.0001=
36<br>
=A087,0.02109821,-0.01736395,0.01944399,-0.00592881,-0.00210692,0.0062065<b=
r>=A03,0.00016140,-0.00031015,0.00163526,-0.12224127,0.02923142,-0.01828769=
<br>=A0,-0.00706340,0.00792232,-0.01103228,0.40012671,-0.00096104,-0.000604=
22<br>
=A0,-0.00036248,-0.00093821,-0.00143622,-0.00088626,0.00007269,0.00015152<b=
r>=A0,0.00006837,-0.00249857,-0.01283405,0.01777286,-0.00009676,0.00026276,=
<br>=A0-0.00126723,0.00201492,0.00185551,-0.00529269,0.04481640,-0.12800032=
,0<br>
......<br clear=3D"all"><div><br>-- <br>Dr. Partha Sarathi Sengupta<br>Asso=
ciate Professor<br>Vivekananda Mahavidyalaya, Burdwan
</div></div></div></div>
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