From owner-chemistry@ccl.net Mon Jul 23 04:04:01 2012 From: "sobereva sobjubao++yahoo.com.cn" To: CCL Subject: CCL: Visualization software that exports U3D format files Message-Id: <-47263-120723040311-31248-TLelH+xv4CTQ1FzsQAYAGQ.@.server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 23 Jul 2012 16:02:57 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao++yahoo.com.cn] Hi, VMD may be able to achieve your goal, please consult http://www.ks.uiuc.edu/Research/vmd/minitutorials/acrobat3d/ Tian Lu --- On Fri, 7/20/12, Jim Kress ccl_nospam^_^kressworks.com wrote: > From: Jim Kress ccl_nospam^_^kressworks.com > Subject: CCL: Visualization software that exports U3D format files > To: "Lu, Tian " > Date: Friday, July 20, 2012, 11:27 PM > > Sent to CCL by: "Jim Kress" [ccl_nospam!A!kressworks.com] > Anyone know of any molecular visualization software that > exports 3D > molecular visualization data to U3D format?  I need to > embed 3D, > manipulatable objects into PDF files and this is the only > path (of which I > am aware) to do this. > > Thanks. > > Jim Kress > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the !=! sign. You > can also> > E-mail to subscribers: CHEMISTRY!=!ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST!=!ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Mon Jul 23 07:13:00 2012 From: "Prashant kumar prashantkbio**gmail.com" To: CCL Subject: CCL: Electrostatic interaction energy! Message-Id: <-47264-120723071202-16078-9/BO6zVaZTSJV6IXPsFC1g[A]server.ccl.net> X-Original-From: "Prashant kumar" Date: Mon, 23 Jul 2012 07:11:59 -0400 Sent to CCL by: "Prashant kumar" [prashantkbio|,|gmail.com] Dear CCLers, I am performing some electrostatic calculation for certain small molecule dimer's using different force field method. But I am just wondering does there any tool to calculate electrostatic using MMFF94. I'd greatly appreciate any suggestion. Thanks, P. From owner-chemistry@ccl.net Mon Jul 23 11:05:00 2012 From: "M Shabbir shabbir193rb-$-gmail.com" To: CCL Subject: CCL: Highlighting some part of a molecule Message-Id: <-47265-120721015610-31125-P3pW5FHh/kt/o+GtubpMsA]|[server.ccl.net> X-Original-From: "M Shabbir" Date: Sat, 21 Jul 2012 01:56:07 -0400 Sent to CCL by: "M Shabbir" [shabbir193rb!=!gmail.com] Dear Dr.McCann, Thanks for ur comments. Although by selecting from atomic list some atoms become highlighted BUT my aim is to change their color or just highlight these in this way without any numbering as shown on atoms by default... Dr.Shabbir Osaka University,Japan > "Billy McCann bwm0005]*[tigermail.auburn.edu" wrote: > > Sent to CCL by: Billy McCann [bwm0005]-[tigermail.auburn.edu] > > Hello Dr. Shabbir, > > In Gaussview, you can select Edit > Atom list. From there, you'll get the atom list for which there is a "highlight" column. Just select the atom(s) you'd like to highlight and click on the corresponding cell. I don't think that the highlight color is configurable. I'm using GaussView5 for Windows. > > Hope that helps. > > +++++++++++++++++++++++++ > Billy Wayne McCann > Ph.D. Candidate > Orlando Acevedo Reseach > Auburn University, Alabama > Office # = 334.844.6948 > bwayne on irc.freenode.net > +++++++++++++++++++++++++ > > -----Original Message----- > > From: owner-chemistry+bwm0005==auburn.edu*ccl.net [mailto:owner- chemistry+bwm0005==auburn.edu*ccl.net] On Behalf Of M Shabbir shabbir193rb{:}gmail.com > Sent: Friday, July 20, 2012 9:26 AM > To: Billy McCann > Subject: CCL: Highlighting some part of a molecule > > > Sent to CCL by: "M Shabbir" [shabbir193rb~~gmail.com] Dear CCL colleagues, > > How is it possible by using (GuessView or Macmolepro etc.) to highlight some specific atoms in a molecule? > > Thanks in advance! > regards, > > Dr.Shabbirhttp://www.ccl.net/cgi- bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammer s.txt > From owner-chemistry@ccl.net Mon Jul 23 11:40:00 2012 From: "Priyanka Goud priyankagoud8__gmail.com" To: CCL Subject: CCL:G: Job Stops In middle without any error. Message-Id: <-47266-120723100010-7150-LYchV2S8oOHJJUMg3bIvPA=-=server.ccl.net> X-Original-From: Priyanka Goud Content-Type: multipart/alternative; boundary=14dae934107954e38e04c57fa9b0 Date: Mon, 23 Jul 2012 19:29:59 +0530 MIME-Version: 1.0 Sent to CCL by: Priyanka Goud [priyankagoud8_-_gmail.com] --14dae934107954e38e04c57fa9b0 Content-Type: text/plain; charset=ISO-8859-1 Dear all, I have been running Counterpoise calculations for BSSE corrections for B2PLYPD/ basis set (6-311G(d,p)) for C N H and 6-311G(3df,3pd) for sulphur using * GAUSSIAN09* of a dimer having a total number of atoms greater than 100 . JOb suddenly stops after running for nearly 12 hours. I have checked using changing RAM size and scratch space. In fact I used %mem=32000mb %nprochared=16 %lindaworkers=ibnode1:1,ibnode2:1,ibnode3:1,ibnode4:1 and %mem=36000mb %nprochared=12 %lindaworkers=ibnode1:1,ibnode2:1,ibnode3:1,ibnode4:1 and %mem=32000mb %nprochared=8 %lindaworkers=ibnode1:1,ibnode2:1,ibnode3:1,ibnode4:1 having a 1.2 terabyte scratch space in each node. *when job stops there is half of the scratch space still left. * In all the cases the jobs stops at the same line. Here is the starting input #T b2plypd/gen counterpoise=2 central- 0,1 0,1 0,1 S 4.67960000 12.06400000 1.62290000 1 S 8.06260000 12.89380000 -1.09170000 1 S 5.61210000 14.94350000 -3.74360000 1 N 7.28740000 11.68230000 1.504200001 ..................................... The end of the output file where it get STOPS is Leave Link 801 at Tue Jul 24 08:59:40 2012, MaxMem= 4194304000 cpu: 13.5 (Enter /opt/Apps/g09/linda-exe/l906.exel) DoSCS=T DFT=T ScalE2(SS,OS)= 0.270000 0.270000 FulOut=F Deriv=F AODrv=F NAtomX= 96 MMem= 19 MDisk= 79 MDiskD= 79 W3Min= 210765048 MinDsk= 206509787 NBas6D= 1768 NBas2D= 1566868 NTT= 1563796 LW2= 2000000 MDV= 4187223734 MDiskM= 11836 NBas2p= 604830 Disk-based method using OVN memory for 79 occupieds at a time. Estimated scratch disk usage=220483764618 words. IMap= 1 8 9 16 17 24 25 32 33 40 41 48 49 56 57 64 65 72 73 79 IMap= 2 7 10 15 18 23 26 31 34 39 42 47 50 55 58 63 66 71 74 78 IMap= 3 6 11 14 19 22 27 30 35 38 43 46 51 54 59 62 67 70 75 77 IMap= 4 5 12 13 20 21 28 29 36 37 44 45 52 53 60 61 68 69 76 IMap= 1 8 9 16 17 24 25 32 33 40 41 48 49 56 57 64 65 72 73 79 IMap= 2 7 10 15 18 23 26 31 34 39 42 47 50 55 58 63 66 71 74 78 IMap= 3 6 11 14 19 22 27 30 35 38 43 46 51 54 59 62 67 70 75 77 IMap= 4 5 12 13 20 21 28 29 36 37 44 45 52 53 60 61 68 69 76 IMap= 1 8 9 16 17 24 25 32 33 40 41 48 49 56 57 64 65 72 73 79 IMap= 2 7 10 15 18 23 26 31 34 39 42 47 50 55 58 63 66 71 74 78 IMap= 3 6 11 14 19 22 27 30 35 38 43 46 51 54 59 62 67 70 75 77 IMap= 4 5 12 13 20 21 28 29 36 37 44 45 52 53 60 61 68 69 76 IMap= 1 8 9 16 17 24 25 32 33 40 41 48 49 56 57 64 65 72 73 79 IMap= 2 7 10 15 18 23 26 31 34 39 42 47 50 55 58 63 66 71 74 78 IMap= 3 6 11 14 19 22 27 30 35 38 43 46 51 54 59 62 67 70 75 77 IMap= 4 5 12 13 20 21 28 29 36 37 44 45 52 53 60 61 68 69 76 Actual scratch disk usage=216872685450 words. Actual scratch disk usage=216872685450 words. JobTyp=1 Pass 1: I= 41 to 60 NPSUse= 8 ParTrn=T ParDer=T DoDerP=F. JobTyp=1 Pass 1: I= 61 to 79 NPSUse= 8 ParTrn=T ParDer=T DoDerP=F. Actual scratch disk usage=216872685450 words. JobTyp=1 Pass 1: I= 21 to 40 NPSUse= 8 ParTrn=T ParDer=T DoDerP=F. Actual scratch disk usage=216872685450 words. JobTyp=1 Pass 1: I= 1 to 20 NPSUse= 8 ParTrn=T ParDer=T DoDerP=F. Can anyone kindly suggest what is going wrong with this. -- *With Regards*, B.Priyanka, Research Scholar, Computational Chemistry, IICT,Habsiguda, India. --14dae934107954e38e04c57fa9b0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable



Dear all,
=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I have been = running Counterpoise calculations for BSSE corrections for B2PLYPD/
basi= s set (6-311G(d,p)) for C N H and=A0 6-311G(3df,3pd) for sulphur using G= AUSSIAN09

=A0of a dimer having a total number of atoms greater than 100 .
JOb suddenly stops after running for nearly 12 hours.
I have checked using changing RAM size and scratch space.

In fact I = used
%mem=3D32000mb
%nprochared=3D16
%lindaworkers=3Dibnode1:1,ib= node2:1,ibnode3:1,ibnode4:1

and
%mem=3D36000mb
%nprochared=3D12
%lindaworkers=3Dibnode1:1,ibnode2:1,ibnode3:1,ibnode4:1

and
%mem= =3D32000mb
%nprochared=3D8
%lindaworkers=3Dibnode1:1,ibnode2:1,ibnode3:1,ibnode4:1


having a 1.2 terabyte scratch space in each node.
= when job stops there is half of the scratch space still left.
=
In all the cases the jobs stops at the same line.

Here is th= e starting input=A0
#T=A0 b2plypd/gen counterpoise=3D2

central-

0,1 0,1 0,1
=A0S=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.67960000=A0= =A0 12.06400000=A0=A0=A0 1.62290000 1
=A0S=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 8.06260000=A0=A0 12.89380000=A0=A0 -1.09170000 1=A0S=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 5.61210000=A0= =A0 14.94350000=A0=A0 -3.74360000 1
=A0N=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 7.28740000=A0=A0= 11.68230000=A0=A0=A0 1.504200001
.....................................<= br>


The end of the output file where it get STOPS is=A0

= Leave Link=A0 801 at Tue Jul 24 08:59:40 2012, MaxMem=3D 4194304000 cpu:=A0=A0= =A0=A0=A0 13.5
=A0(Enter /opt/Apps/g09/linda-exe/l906.exel)
=A0DoSCS=3DT DFT=3DT ScalE2= (SS,OS)=3D=A0 0.270000=A0 0.270000
=A0FulOut=3DF Deriv=3DF AODrv=3DF NAt= omX=3D=A0=A0=A0 96
=A0=A0 MMem=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0 19=A0 MDisk= =3D=A0=A0=A0=A0=A0=A0=A0=A0=A0 79 MDiskD=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0 79=A0 W3Min=3D=A0=A0 210765048 MinDsk=3D=A0=A0 206509787 NBas6D=3D=A0=A0=A0= =A0=A0=A0=A0 1768
=A0NBas2D=3D=A0=A0=A0=A0 1566868=A0=A0=A0 NTT=3D=A0=A0=A0=A0 1563796=A0=A0= =A0 LW2=3D=A0=A0=A0=A0 2000000
=A0=A0=A0 MDV=3D=A0 4187223734 MDiskM=3D=A0= =A0=A0=A0=A0=A0 11836 NBas2p=3D=A0=A0=A0=A0=A0 604830
=A0Disk-based meth= od using OVN memory for 79 occupieds at a time.
=A0Estimated scratch disk usage=3D220483764618 words.
=A0IMap=3D=A0=A0 1=A0=A0 8=A0=A0 9=A0 16=A0 17=A0 24=A0 25=A0 32=A0 33=A0 4= 0=A0 41=A0 48=A0 49=A0 56=A0 57=A0 64=A0 65=A0 72=A0 73=A0 79
=A0IMap=3D= =A0=A0 2=A0=A0 7=A0 10=A0 15=A0 18=A0 23=A0 26=A0 31=A0 34=A0 39=A0 42=A0 4= 7=A0 50=A0 55=A0 58=A0 63=A0 66=A0 71=A0 74=A0 78
=A0IMap=3D=A0=A0 3=A0= =A0 6=A0 11=A0 14=A0 19=A0 22=A0 27=A0 30=A0 35=A0 38=A0 43=A0 46=A0 51=A0 = 54=A0 59=A0 62=A0 67=A0 70=A0 75=A0 77
=A0IMap=3D=A0=A0 4=A0=A0 5=A0 12=A0 13=A0 20=A0 21=A0 28=A0 29=A0 36=A0 37= =A0 44=A0 45=A0 52=A0 53=A0 60=A0 61=A0 68=A0 69=A0 76
=A0IMap=3D=A0=A0 = 1=A0=A0 8=A0=A0 9=A0 16=A0 17=A0 24=A0 25=A0 32=A0 33=A0 40=A0 41=A0 48=A0 = 49=A0 56=A0 57=A0 64=A0 65=A0 72=A0 73=A0 79
=A0IMap=3D=A0=A0 2=A0=A0 7= =A0 10=A0 15=A0 18=A0 23=A0 26=A0 31=A0 34=A0 39=A0 42=A0 47=A0 50=A0 55=A0= 58=A0 63=A0 66=A0 71=A0 74=A0 78
=A0IMap=3D=A0=A0 3=A0=A0 6=A0 11=A0 14=A0 19=A0 22=A0 27=A0 30=A0 35=A0 38= =A0 43=A0 46=A0 51=A0 54=A0 59=A0 62=A0 67=A0 70=A0 75=A0 77
=A0IMap=3D= =A0=A0 4=A0=A0 5=A0 12=A0 13=A0 20=A0 21=A0 28=A0 29=A0 36=A0 37=A0 44=A0 4= 5=A0 52=A0 53=A0 60=A0 61=A0 68=A0 69=A0 76
=A0IMap=3D=A0=A0 1=A0=A0 8= =A0=A0 9=A0 16=A0 17=A0 24=A0 25=A0 32=A0 33=A0 40=A0 41=A0 48=A0 49=A0 56= =A0 57=A0 64=A0 65=A0 72=A0 73=A0 79
=A0IMap=3D=A0=A0 2=A0=A0 7=A0 10=A0 15=A0 18=A0 23=A0 26=A0 31=A0 34=A0 39= =A0 42=A0 47=A0 50=A0 55=A0 58=A0 63=A0 66=A0 71=A0 74=A0 78
=A0IMap=3D= =A0=A0 3=A0=A0 6=A0 11=A0 14=A0 19=A0 22=A0 27=A0 30=A0 35=A0 38=A0 43=A0 4= 6=A0 51=A0 54=A0 59=A0 62=A0 67=A0 70=A0 75=A0 77
=A0IMap=3D=A0=A0 4=A0= =A0 5=A0 12=A0 13=A0 20=A0 21=A0 28=A0 29=A0 36=A0 37=A0 44=A0 45=A0 52=A0 = 53=A0 60=A0 61=A0 68=A0 69=A0 76
=A0IMap=3D=A0=A0 1=A0=A0 8=A0=A0 9=A0 16=A0 17=A0 24=A0 25=A0 32=A0 33=A0 4= 0=A0 41=A0 48=A0 49=A0 56=A0 57=A0 64=A0 65=A0 72=A0 73=A0 79
=A0IMap=3D= =A0=A0 2=A0=A0 7=A0 10=A0 15=A0 18=A0 23=A0 26=A0 31=A0 34=A0 39=A0 42=A0 4= 7=A0 50=A0 55=A0 58=A0 63=A0 66=A0 71=A0 74=A0 78
=A0IMap=3D=A0=A0 3=A0= =A0 6=A0 11=A0 14=A0 19=A0 22=A0 27=A0 30=A0 35=A0 38=A0 43=A0 46=A0 51=A0 = 54=A0 59=A0 62=A0 67=A0 70=A0 75=A0 77
=A0IMap=3D=A0=A0 4=A0=A0 5=A0 12=A0 13=A0 20=A0 21=A0 28=A0 29=A0 36=A0 37= =A0 44=A0 45=A0 52=A0 53=A0 60=A0 61=A0 68=A0 69=A0 76
=A0Actual=A0=A0= =A0 scratch disk usage=3D216872685450 words.
=A0Actual=A0=A0=A0 scratch = disk usage=3D216872685450 words.
=A0JobTyp=3D1 Pass=A0 1:=A0 I=3D=A0 41 = to=A0 60 NPSUse=3D=A0 8 ParTrn=3DT ParDer=3DT DoDerP=3DF.
=A0JobTyp=3D1 Pass=A0 1:=A0 I=3D=A0 61 to=A0 79 NPSUse=3D=A0 8 ParTrn=3DT P= arDer=3DT DoDerP=3DF.
=A0Actual=A0=A0=A0 scratch disk usage=3D2168726854= 50 words.
=A0JobTyp=3D1 Pass=A0 1:=A0 I=3D=A0 21 to=A0 40 NPSUse=3D=A0 8= ParTrn=3DT ParDer=3DT DoDerP=3DF.
=A0Actual=A0=A0=A0 scratch disk usage= =3D216872685450 words.
=A0JobTyp=3D1 Pass=A0 1:=A0 I=3D=A0=A0 1 to=A0 20 NPSUse=3D=A0 8 ParTrn=3DT= ParDer=3DT DoDerP=3DF.




Can anyone kindly suggest what i= s going wrong with this.


-- With Regards,

B.Priyanka,
Research Scholar,
Computational Chemistry,
IICT,Habsiguda,
India.
--14dae934107954e38e04c57fa9b0-- From owner-chemistry@ccl.net Mon Jul 23 12:50:00 2012 From: "Jesse A. Gordon jesse.gordon]*[dotmatics.com" To: CCL Subject: CCL: Invitation to Webinar chemical scaffold and R-Group analyses Message-Id: <-47267-120723124453-4944-tcVvgveEkyQWMrPBBYS+vQ^^server.ccl.net> X-Original-From: "Jesse A. Gordon" Date: Mon, 23 Jul 2012 12:44:51 -0400 Sent to CCL by: "Jesse A. Gordon" [jesse.gordon^^dotmatics.com] We invite you to attend our complimentary webinars to learn more about Dotmatics solutions. Next week's upcoming webinar: "Simple and Efficient Tools for Chemists Introducing Dotmatics for Office and Vortex" Focusing on: * Dotmatics applications were designed from the ground up, by scientists for scientists. In this webinar we will review how chemical structures can be used in conjunction with data visualization in Vortex. * The ability to display and share chemical data and structures via Microsoft Excel, Word, Powerpoint and Outlook will also be demonstrated. * Vortex provides visualization and analysis for chemical and biological data, including scatterplots, barcharts, pie charts, radar plots, and... * R-Group analysis (organizing physiochemical data by automatically extracted R-groups from a specified skeleton) * Scaffold analysis (extracting and comparing rings and connectors) * K-Means Clustering (assign fingerprints by atom or fragment characteristiics, for both Tanimoto and Rogers-Tanimoto similarity, then cluster by distance from chemical centroids). * Register for early on July 19: (Thursday 6AM PT / 9AM ET / 2PM BST / 3PM CET ): https://www2.gotomeeting.com/register/391789074 * Register for late on July 19: (Thursday 10AM PT / 1PM ET / 6PM BST / 7PM CET): https://www2.gotomeeting.com/register/173468314 * Register to book your spot for other live webinars to hear from the experts: http://www.dotmatics.com/webinars/ From owner-chemistry@ccl.net Mon Jul 23 13:25:00 2012 From: "Geoffrey Hutchison geoffh _ pitt.edu" To: CCL Subject: CCL: Electrostatic interaction energy! Message-Id: <-47268-120723131830-20914-fmzZuN+0ToVi1dYFAsVp/A]_[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Mon, 23 Jul 2012 13:18:20 -0400 MIME-version: 1.0 (Mac OS X Mail 6.0 \(1482\)) Sent to CCL by: Geoffrey Hutchison [geoffh|pitt.edu] > I am performing some electrostatic calculation for certain small molecule > dimer's using different force field method. But I am just wondering does there > any tool to calculate electrostatic using MMFF94. I'd greatly appreciate any > suggestion. It's quite easy to compute partial charges using the MMFF94 charge model using Open Babel: obabel (filename) --partialcharge MMFF94 -O (newfilename).mol2 where (filename) is whatever file you want to parse. One key element is using the Sybyl mol2 format (newfilename).mol2 since this includes partial charges in the final column. Of course other file formats will work too. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh- -pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Mon Jul 23 14:36:00 2012 From: "Prashant Kumar prashantkbio---gmail.com" To: CCL Subject: CCL: Electrostatic interaction energy! Message-Id: <-47269-120723143433-24020-mHhZ81fx1BepI80WDFk49w,+,server.ccl.net> X-Original-From: Prashant Kumar Content-Type: multipart/alternative; boundary=bcaec54c527cca0a1904c5837ed1 Date: Mon, 23 Jul 2012 20:34:05 +0200 MIME-Version: 1.0 Sent to CCL by: Prashant Kumar [prashantkbio.:.gmail.com] --bcaec54c527cca0a1904c5837ed1 Content-Type: text/plain; charset=ISO-8859-1 Dear Prof. Geoffrey, Thank you for your suggestion, my objective is not only obtain partial charge from MMFF94 but compute electrostatic interaction energy between particular dimer's. I did for GAFF using mm-pbsa from Amber-tools. I like to perform same calculation but using MMFF94. Best, P. On Mon, Jul 23, 2012 at 7:18 PM, Geoffrey Hutchison geoffh _ pitt.edu < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: Geoffrey Hutchison [geoffh|pitt.edu] > > > I am performing some electrostatic calculation for certain small molecule > > dimer's using different force field method. But I am just wondering does > there > > any tool to calculate electrostatic using MMFF94. I'd greatly appreciate > any > > suggestion. > > It's quite easy to compute partial charges using the MMFF94 charge model > using Open Babel: > obabel (filename) --partialcharge MMFF94 -O (newfilename).mol2 > > where (filename) is whatever file you want to parse. One key element is > using the Sybyl mol2 format (newfilename).mol2 since this includes partial > charges in the final column. Of course other file formats will work too. > > Hope that helps, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh=-=pitt.edu > web: http://hutchison.chem.pitt.edu/> > > --bcaec54c527cca0a1904c5837ed1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Prof. Geoffrey,


Thank you for your s= uggestion, my objective is not only obtain partial charge from MMFF94 but c= ompute electrostatic interaction energy between=A0particular=A0dimer's.= I did for GAFF using mm-pbsa from=A0Amber-tools. I like to perform same ca= lculation but using MMFF94.=A0

Best,

P.=A0

On Mon, Jul 23, 2012 at 7:18 PM, Geoffrey Hutchison geoffh= _ pitt.edu <owner-chemistry###ccl.n= et> wrote:

Sent to CCL by: Geoffrey Hutchison [geoffh|pitt.edu]

> I am performing some electrostatic calculation for certain small molec= ule
> dimer's using different force field method. But I am just wonderin= g does there
> any tool to calculate electrostatic using MMFF94. I'd greatly appr= eciate any
> suggestion.

It's quite easy to compute partial charges using the MMFF94 charg= e model using Open Babel:
obabel (filename) --partialcharge MMFF94 -O (newfilename).mol2

where (filename) is whatever file you want to parse. One key element is usi= ng the Sybyl mol2 format (newfilename).mol2 since this includes partial cha= rges in the final column. Of course other file formats will work too.

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh=3D-=3Dpitt.edu<= /a>
web: http://h= utchison.chem.pitt.edu/



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--bcaec54c527cca0a1904c5837ed1-- From owner-chemistry@ccl.net Mon Jul 23 18:59:00 2012 From: "Jesse Gordon jesse.gordon+/-dotmatics.com" To: CCL Subject: CCL: Webinar: Chemical scaffold, similarity, and R-Group analyses in Vortex Message-Id: <-47270-120723124338-4182-XNg463HsvSwtRVy3dbHhHQ : server.ccl.net> X-Original-From: Jesse Gordon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Mon, 23 Jul 2012 12:43:29 -0400 MIME-Version: 1.0 Sent to CCL by: Jesse Gordon [jesse.gordon-,-dotmatics.com] We invite you to attend our complimentary webinars to learn more about Dotmatics solutions. Next week's upcoming webinar: "Simple and Efficient Tools for Chemists – Introducing Dotmatics for Office and Vortex" Focusing on: * Dotmatics’ applications were designed from the ground up, by scientists for scientists. In this webinar we will review how chemical structures can be used in conjunction with data visualization in Vortex. * The ability to display and share chemical data and structures via Microsoft Excel, Word, Powerpoint and Outlook will also be demonstrated. * Vortex provides visualization and analysis for chemical and biological data, including scatterplots, barcharts, pie charts, radar plots, and... * R-Group analysis (organizing physiochemical data by automatically extracted R-groups from a specified skeleton) * Scaffold analysis (extracting and comparing rings and connectors) * K-Means Clustering (assign fingerprints by atom or fragment characteristiics, for both Tanimoto and Rogers-Tanimoto similarity, then cluster by distance from chemical centroids). * Register for early on July 19: (Thursday 6AM PT / 9AM ET / 2PM BST / 3PM CET ): https://www2.gotomeeting.com/register/391789074 * Register for late on July 19: (Thursday 10AM PT / 1PM ET / 6PM BST / 7PM CET): https://www2.gotomeeting.com/register/173468314 * Register to book your spot for other live webinars to hear from the experts: http://www.dotmatics.com/webinars/ -- ===================================== Jesse Gordon Application Scientist Dotmatics Inc. 400 West Cummings Park #5450, Woburn MA 01801 T: +1 781-305-3114 M: +1-617-320-6989 Email: jesse.gordon##dotmatics.com Skype: jessegordon ====================================== Dotmatics Providing Informatics for Everyone See the latest in Dotmatics Suite of Solutions: Booth #1708 at the 244th ACS Meeting , August 19-21, 2012, Philadelphia PA Reserve your spot in the upcoming LIVE webinar series: http://www.dotmatics.com/webinars/ -- Disclaimer: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. Dotmatics Limited screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. Dotmatics Limited accepts no liability for any damage caused by any virus transmitted by this electronic mail. Dotmatics Limited is registered in England & Wales No. 5614524 with offices at The Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. From owner-chemistry@ccl.net Mon Jul 23 19:34:00 2012 From: "Andrew Yeung andrew.yeung() chem.tamu.edu" To: CCL Subject: CCL: Highlighting some part of a molecule Message-Id: <-47271-120723140324-22131-nq+HtoafNJs8COnwPoHZuA#server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Jul 2012 13:03:10 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung[-]chem.tamu.edu] You can export the structure as cartesian coordinates (XYZ), and manipulate it with your favorite 3D program like Mercury or Avogadro. If you want nice pictures, you can re-export to POV-Ray and render them. Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-07-21 12:56 AM, M Shabbir shabbir193rb-$-gmail.com wrote: > Sent to CCL by: "M Shabbir" [shabbir193rb!=!gmail.com] > Dear Dr.McCann, > Thanks for ur comments. Although by selecting from atomic list some atoms become highlighted BUT > my aim is to change their color or just highlight these in this way without any numbering as shown on > atoms by default... > > Dr.Shabbir > Osaka University,Japan > > > > >> "Billy McCann bwm0005]*[tigermail.auburn.edu" wrote: >> >> Sent to CCL by: Billy McCann [bwm0005]-[tigermail.auburn.edu] >> >> Hello Dr. Shabbir, >> >> In Gaussview, you can select Edit > Atom list. From there, you'll get the atom list for which there is > a "highlight" column. Just select the atom(s) you'd like to highlight and click on the corresponding cell. > I don't think that the highlight color is configurable. I'm using GaussView5 for Windows. >> Hope that helps. >> >> +++++++++++++++++++++++++ >> Billy Wayne McCann >> Ph.D. Candidate >> Orlando Acevedo Reseach >> Auburn University, Alabama >> Office # = 334.844.6948 >> bwayne on irc.freenode.net >> +++++++++++++++++++++++++ >> >> -----Original Message----- >>> From: owner-chemistry+bwm0005==auburn.edu*ccl.net [mailto:owner- > chemistry+bwm0005==auburn.edu*ccl.net] On Behalf Of M Shabbir shabbir193rb{:}gmail.com >> Sent: Friday, July 20, 2012 9:26 AM >> To: Billy McCann >> Subject: CCL: Highlighting some part of a molecule >> >> >> Sent to CCL by: "M Shabbir" [shabbir193rb~~gmail.com] Dear CCL colleagues, >> >> How is it possible by using (GuessView or Macmolepro etc.) to highlight some specific atoms in a > molecule? >> Thanks in advance! >> regards, >> >> Dr.Shabbirhttp://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammer > s.txt> >