From owner-chemistry@ccl.net Tue Jun 13 01:10:00 2006 From: "Steven ccl*o*mail.sioc.ac.cn" To: CCL Subject: CCL: Reg: 2D to 3D conversion Message-Id: <-31933-060613010706-32595-ntwKXwevNA41u2MfvPtvZA|-|server.ccl.net> X-Original-From: "Steven" Content-Type: Multipart/related; type="multipart/alternative"; boundary="------------Boundary-00=_4U8SQL80000000000000" Date: Tue, 13 Jun 2006 13:06:04 +0800 MIME-Version: 1.0 Sent to CCL by: "Steven" [ccl[A]mail.sioc.ac.cn] --------------Boundary-00=_4U8SQL80000000000000 Content-Type: Multipart/Alternative; boundary="------------Boundary-00=_4U8SLVC0000000000000" --------------Boundary-00=_4U8SLVC0000000000000 Content-Type: Text/Plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi, Krishnamurthy,=0D =0D CONCORD and CORINA are two popular 2D->3D converting programs. You can f= ind some details in the review article "Sadowski J.; Gasteiger, J.; From Atom= s and Bonds to Three-Dimensional Atomic Coordinates:Automatic Model Builder= s, Chem. Rev. 1993, 93. 2567-2581".=0D =0D I hope it can give you some help.=0D =0D Best wishes,=0D =0D Yuan Zhao.=0D =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0D State Key Lab of Bio-organic and Natural Products Chemistry =0D Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Scienc= es.=0D Addr. 354, Fenglin Road, Shanghai, China.=0D Tel.: +86-21-54925275=0D Email: yzhao]^[mail.sioc.ac.cn=0D -------Original Message-------=0D =0D > From: Anand Krishnamurthy anand{=3D}loyolacollege.edu=0D Date: 06/12/06 21:27:23=0D To: Wang, Renxiao =0D Subject: CCL: Reg: 2D to 3D conversion=0D =0D Sent to CCL by: "Anand Krishnamurthy" [anand ~~ loyolacollege.edu]=0D Greeeting to one and all,=0D =0D I have really been benefitted extensively from an update to mechanise man= y problems on computational chemistry. I would like to know the algorithm involved in converting a two dimensional molecular structure data file i= nto a three dimensional one.Another question is that how do I calculate manua= lly gasteiger charges for small molecules and further can I automate to place charges on all of the similar atoms in molecules.=0D =0D =0D Thanks and regards=0D Anand=0D =0D =0D =0D -=3D This is automatically added to each message by the mailing script =3D= -=0D=0D=0D=0D =0D=0D=0D =0D=0D=0D =0D Subscribe/Unsubscribe:=0D=0D =0D=0D =0D Job: http://www.ccl.net/jobs=0D=0D =0D= =0D =0D=0D=0D =0D=0D =0D=0D =0D =0D =20 --------------Boundary-00=_4U8SLVC0000000000000 Content-Type: Text/HTML; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Hi, Krishnamurthy,
 
CONCORD and CORINA are two popular 2D->3D converting program= s.  You can find some details in the review article "Sadowski J.; Ga= steiger, J.; From Atoms and Bonds to Three-Dimensional Atomic Coordinates= :Automatic Model Builders, Chem. Rev. 1993, 93. 2567-2581".
 
I hope it can give you some help.
 
Best wishes,
 
Yuan Zhao.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
State Key Lab of Bio-organic and = Natural Products Chemistry
Shanghai Institute of Organic Chemistry (S= IOC), Chinese Academy of Sciences.
Addr. 354, Fenglin Road, Shanghai, = China.
Tel.: +86-21-54925275
Email: yzhao]^[mail.sioc.ac.cn
-------Original Message-------
 
Date: 06/12/06 21:= 27:23
Subject: CCL: Reg:= 2D to 3D conversion
 
Sent to CCL by: "Anand  Krishnamurthy" [anand ~~ loyolacol= lege.edu]
Greeeting to one and all,
 
I have really been benefitted extensively from an update to mechanis= e many problems on computational chemistry. I would like to know the algo= rithm involved in converting  a two dimensional molecular struc= ture data file into a three dimensional one.Another question is that how = do I calculate manually gasteiger charges for small molecules and further= can I automate to place charges on all of the similar atoms in molecules= =2E
 
 
Thanks and regards
Anand
 
 
 
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<-31934-060613035905-20565-DUcROUZqAAanpwYwt3FuqA**server.ccl.net> X-Original-From: "Elie Cohen" Date: Tue, 13 Jun 2006 03:59:03 -0400 Sent to CCL by: "Elie Cohen" [elie|,|molecular-conceptor.com] Synergix Ltd. is pleased to announce the release of Molecular Conceptor v2.6 Molecular Conceptor is a computer-based course for teaching rational drug design, molecular modeling and cheminformatics. Click here to review the NEW table of contents. http://www.molecular-conceptor.com/toc.html I invite you to get more details from our website: http://www.molecular-conceptor.com PS:if you want to be involved in the development of a new chapter, thanks you to send me an email describing your interests and possible contributions. Elie Cohen elie**molecular-conceptor.com Project Leader Molecular Conceptor From owner-chemistry@ccl.net Tue Jun 13 07:56:00 2006 From: "Mahmud Jelill mjelill##hiroshima-u.ac.jp" To: CCL Subject: CCL: Tij ???? Message-Id: <-31935-060613075159-14231-Syki4vbhKk85DmoW2h2ghQ||server.ccl.net> X-Original-From: "Mahmud Jelill" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0023_01C68F2B.371AB260" Date: Tue, 13 Jun 2006 20:51:59 +0900 MIME-Version: 1.0 Sent to CCL by: "Mahmud Jelill" [mjelill]-[hiroshima-u.ac.jp] This is a multi-part message in MIME format. ------=_NextPart_000_0023_01C68F2B.371AB260 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear CCL members, I will very much appreciate if somebody helps to explain what is mean = that the term Tij in OSS2 potential models (L.Ojamae, I.Shavitt, and S = J Singer,J. Chem. Phys.,109, 1998) for solvated proton in water .Could = someone point me to free monte carlo code supporting OSS2/OSS3 = potentials?=20 thanks in advance, M. J. Kokbilge ------=_NextPart_000_0023_01C68F2B.371AB260 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear CCL members,
 
I will very much appreciate if somebody helps to = explain what=20 is mean that the term Tij  in = OSS2 potential=20 models (L.Ojamae, I.Shavitt, and S J Singer,J. Chem. Phys.,109, 1998) = for=20 solvated proton in water .Could someone point me to free monte = carlo=20 code supporting OSS2/OSS3 potentials?=20
 
thanks in advance,
 
M. J.=20 Kokbilge
------=_NextPart_000_0023_01C68F2B.371AB260-- From owner-chemistry@ccl.net Tue Jun 13 09:40:00 2006 From: "kiran yvkiran**rediffmail.com" To: CCL Subject: CCL: Reg: 2D to 3D conversion Message-Id: <-31936-060612154211-15585-/5skQuMtzqQRhsvn7AvhcQ*_*server.ccl.net> X-Original-From: "kiran" Content-type: multipart/alternative; boundary="Next_1150134794---0-203.199.83.245-4371" Date: 12 Jun 2006 17:53:14 -0000 MIME-Version: 1.0 Sent to CCL by: "kiran" [yvkiran-$-rediffmail.com] This is a multipart mime message --Next_1150134794---0-203.199.83.245-4371 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Anand sir,=0A=0AYou can either use cornia or Concord for converting th= e 2D structures to 3D ones. But you can get only one conformation of the st= ructure. The online version of cornia will be helpful in converting 1000 st= rucutres free for you. I think for you second question Tinker software may = be useful. There are plenty of other softwares available which have applica= tions in Linux platform only. =0A=0ARegards,=0AVishwakiran =A0=0A=0A=0AOn M= on, 12 Jun 2006 Anand Krishnamurthy anand{=3D}loyolacollege.edu wrote :=0A>= Sent to CCL by: "Anand Krishnamurthy" [anand ~~ loyolacollege.edu]=0A>Gree= eting to one and all,=0A>=0A>I have really been benefitted extensively from= an update to mechanise many problems on computational chemistry. I would l= ike to know the algorithm involved in converting a two dimensional molecul= ar structure data file into a three dimensional one.Another question is tha= t how do I calculate manually gasteiger charges for small molecules and fur= ther can I automate to place charges on all of the similar atoms in molecul= es.=0A>=0A>=0A>Thanks and regards=0A>Anand=0A>=0A>=0A>=0A>-=3D This is auto= matically added to each message by the mailing script =3D-=0A>To recover th= e email address of the author of the message, please change=0A>the strange = characters on the top line to the -,- sign. You can also=0A>look up the X-Ori= ginal-From: line in the mail header.=0A>=0A>E-mail to subscribers: CHEMISTR= Y-,-ccl.net or use:=0A= =0A>=0A=0A> ==0A>=0A>Subscribe/Unsubscr= ibe:=0A=0A>=0A>Before p= osting, check wait time at: http://www.ccl.net=0A>=0A>Job: http://www.ccl.n= et/jobs=0A>Conferences: http://server.ccl.net/chemistry/announcements/confe= rences/=0A>=0A>Search Messages: http://www.ccl.net/htdig (login: ccl, Pass= word: search)=0A>=0A= =0A=0A>=0A>RTFI: http://www.ccl.net/= chemistry/aboutccl/instructions/=0A>=0A>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+=0A>=0A>=0A>=0A=0A=0AMr.Y.Vishwakiran= =0D=0AHead, Aravinda Biosolutions,=0D=0A325, Kubera Towers,=0D=0ANarayaguda= , Hyderabad=0D=0AINDIA=0D=0APh: +914027240344=0D=0AMobile:+91849150125= =0D=0A=0D=0AEmail: yvkiran-,-yahoo.com=0D=0A yvkiran-,-rediff.com = =20 --Next_1150134794---0-203.199.83.245-4371 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0ADear Anand sir,
=0A
=0AYou can either use cornia or Concord for= converting the 2D structures to 3D ones. But you can get only one conforma= tion of the structure. The online version of cornia will be helpful in conv= erting 1000 strucutres free for you. I think for you second question Tinker= software may be useful. There are plenty of other softwares available whic= h have applications in Linux platform only.
=0A
=0ARegards,
=0AVi= shwakiran 
=0A
=0A
=0AOn Mon, 12 Jun 2006 Anand Krishnamurth= y anand{=3D}loyolacollege.edu wrote :
=0A>Sent to CCL by: "Anand=   Krishnamurthy" [anand ~~ loyolacollege.edu]
=0A>Greeeting= to one and all,
=0A>
=0A>I have really been benefitted extensi= vely from an update to mechanise many problems on computational chemistry. = I would like to know the algorithm involved in converting  a two dimen= sional molecular structure data file into a three dimensional one.Another q= uestion is that how do I calculate manually gasteiger charges for small mol= ecules and further can I automate to place charges on all of the similar at= oms in molecules.
=0A>
=0A>
=0A>Thanks and regards
=0A= >Anand
=0A>
=0A>
=0A>
=0A>-=3D This is automatic= ally added to each message by the mailing script =3D-
=0A>To recover = the email address of the author of the message, please change
=0A>the= strange characters on the top line to the -,- sign. You can also
=0A>l= ook up the X-Original-From: line in the mail header.
=0A>
=0A>E= -mail to subscribers: CHEMISTRY-,-ccl.net or use:
=0A>    &nb= sp;
=0A>
=0A>E= -mail to administrators: CHEMISTRY-REQUEST-,-ccl.net or use
=0A>  =    
=0A>=0A>Subscribe/Unsubscribe:
=0A>      http://www.= ccl.net/chemistry/sub_unsub.shtml
=0A>
=0A>Before posting, chec= k wait time at: http://www.ccl.net
=0A>
=0A>Job: http://www.ccl= .net/jobs
=0A>Conferences: http://server.ccl.net/chemistry/announceme= nts/conferences/
=0A>
=0A>Search Messages: http://www.ccl.net/h= tdig  (login: ccl, Password: search)
=0A>
=0A>If your mail= bounces from CCL with 5.7.1 error, check:
=0A>      =
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=0A>RTFI: http://www.ccl.n= et/chemistry/aboutccl/instructions/
=0A>
=0A>-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
=0A>
=0A>= ;
=0A>
=0A=0A

=0A=0A=0AMr.Y.Vishwakiran=0D
=0AHead, Aravinda=  Biosolutions,=0D
=0A325, Kubera Towers,=0D
=0ANarayaguda, = Hyderabad=0D
=0AINDIA=0D
=0APh:    +914027240344=0D
=0AM= obile:+91849150125=0D
=0A=0D
=0AEmail:  yvkiran-,-yahoo.com=0D
= =0A        yvkiran-,-rediff.com    

=0A= =0A --Next_1150134794---0-203.199.83.245-4371-- From owner-chemistry@ccl.net Tue Jun 13 16:39:01 2006 From: "Mariusz Radon mariusz.radon*|*gmail.com" To: CCL Subject: CCL:G: PCM on a torus Message-Id: <-31937-060613162315-24520-YtojAK7F0qQud68CROfmnw##server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 Jun 2006 21:28:50 +0200 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon+*+gmail.com] On 6/8/06, Steven Bachrach sbachrach+/-trinity.edu wrote: > I would like to perform solvation calculations on a molecule that is a torus (i.e., a doughnut or bagel shape). A PCM calculation using Gaussian-03 failed when constructing the cavity, with an error message: > > AdVTs1: ISph= 454 is engulfed by JSph= 489 but Ae( 454) is not yet zero! > > I am thinking that the problem is that the topology of the necessary cavity is a doughnut (torus), but PCM usesa cavity that must be topologically related to the sphere. Am I correct in this? Is there some way to do this type of computation? (One idea I have is to place a few explicit solvent molecules in the interior, filling it up, thereby removing the hole so the cavity can then be of spherical topology.) I have reported sth similar at CCL -- please look at: http://www.ccl.net/cgi-bin/ccl/message-new?2006+03+02+003 I don't think this is fundamental problem with PCM, related to molecule topology -- it seems to be rather technical one, but I may be wrong of course. Best wishes, Mariusz Radon