From owner-chemistry@ccl.net Fri Apr 30 01:13:00 2010 From: "allouche * lasim.univ-lyon1.fr" To: CCL Subject: CCL:G: [GaussView] Can GaussView 5 draw the ECD spectra directly? Message-Id: <-41758-100430010916-28016-K4obge8o3tcACbMWpQQCSw^server.ccl.net> X-Original-From: allouche:-:lasim.univ-lyon1.fr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 30 Apr 2010 07:09:09 +0200 MIME-Version: 1.0 Sent to CCL by: allouche*_*lasim.univ-lyon1.fr Hello, Gabedit can do it. Gabedit is a free open source program. You can download it from : gabedit.sourceforge.net A.R. Allouche > > Sent to CCL by: xunlei ding [dingxunlei(a)gmail.com] > Dear All, > > I want to simulate an ECD spectra by G03 with TDDFT calculations. > Can it be shown in GaussView 5 ? > Or how can I draw it from the log file of G03? > > Thank you! > -------------------------------------------------------------------------- Ce message a été envoyé depuis le webmail IMP (Internet Messaging Program) From owner-chemistry@ccl.net Fri Apr 30 02:43:00 2010 From: "xunlei ding dingxunlei!=!gmail.com" To: CCL Subject: CCL:G: [GaussView] Can GaussView 5 draw the ECD spectra directly? Message-Id: <-41759-100430023718-14344-8kYPQipGRdZwBT9ElcxU0A],[server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 30 Apr 2010 14:37:09 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei-*-gmail.com] Thank you very much! I have tried it, and It works well! Best regards, Ding 2010/4/30 allouche * lasim.univ-lyon1.fr : > > Sent to CCL by: allouche*_*lasim.univ-lyon1.fr > Hello, > > Gabedit can do it. > Gabedit is a free open source program. > You can download it from : gabedit.sourceforge.net > > A.R. Allouche > >> >> Sent to CCL by: xunlei ding [dingxunlei(a)gmail.com] >> Dear All, >> >> I want to simulate an ECD spectra by G03 with TDDFT calculations. >> Can it be shown in GaussView 5 ? >> Or how can I draw it from the log file of G03? >> >> Thank you! >> > > -------------------------------------------------------------------------= - > Ce message a =E9t=E9 envoy=E9 depuis le webmail IMP (Internet Messaging P= rogram) From owner-chemistry@ccl.net Fri Apr 30 05:40:00 2010 From: "Tristan Youngs t.youngs|a|qub.ac.uk" To: CCL Subject: CCL: Aten v1.5 released. Message-Id: <-41760-100430045157-18353-ml7wDo7lnGCCvO5H0WS/1A-*-server.ccl.net> X-Original-From: "Tristan Youngs" Date: Fri, 30 Apr 2010 04:51:56 -0400 Sent to CCL by: "Tristan Youngs" [t.youngs|,|qub.ac.uk] Dear CCL, For those who are interested, the atomic configuration editor/tweaker Aten is now up to version 1.5, and has another new website to go with it (approximately 95% less php weight than before!). Many bugs have been fixed, new features have been added, and some 'stuff now works'. Preliminary support for GROMACs files has been added, but probably needs some work. Packages are available for Mac, Windows, and Linux from www.projectaten.net. Thoughts and comments welcome! Cheers, Tris. From owner-chemistry@ccl.net Fri Apr 30 09:17:00 2010 From: "Esther sala.esther.:.gmail.com" To: CCL Subject: CCL: Protein structure prediction through fold recognition Message-Id: <-41761-100430050253-24978-I0K0chKeLNzqgwms3dArRQ{}server.ccl.net> X-Original-From: Esther Content-Type: multipart/alternative; boundary=00163625717542c16404856f9277 Date: Fri, 30 Apr 2010 09:55:48 +0200 MIME-Version: 1.0 Sent to CCL by: Esther [sala.esther]^[gmail.com] --00163625717542c16404856f9277 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jian Wang, you could use PRIME modul from Schr=F6dinger software. It's not free, but a= ll the modules from this company are really competitive and the help support it's very good. http://www.schrodinger.com/ Best regards, Esther On Thu, Apr 29, 2010 at 3:48 PM, Jian Wang computationalboy . gmail.com < owner-chemistry-#-ccl.net> wrote: > > Dear all: > Can anyone recommend some program for protein fold recognition from a > primary sequence? > I can not find good homology protein for my target sequence. > Thanks in advance! > > > -- > Jian Wang (Arthur) > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: computationalboy(at)gmail.com > > --=20 Esther Sala Arg=FCello, PhD student. Nutrigenomics Research Group Biochemistry & Biotechnology Department Universitat Rovira i Virgili Lab 111 Phone +34 977558486 C/Marcel=B7l=ED Domingo s/n 43007 Tarragona (Catalonia, Spain) --00163625717542c16404856f9277 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jian Wang,

you could use PRIME modul from Schr=F6dinger softwar= e. It's not free, but all the modules from this company are really comp= etitive and the help support it's very good.

http://www.schrodinger.com/

Best regards,

Esther

On Thu, A= pr 29, 2010 at 3:48 PM, Jian Wang computationalboy . gmail.com <owner-chemistry-#-ccl.net> wrote:

Dear all:
Can anyone recommend some program for protein f= old recognition from a primary sequence?
I can not find good homology protein for my target sequence.
Thanks in advance!


--
Jian Wang (Arthur)
Shenyang Pharmaceutical University P.O. Bo= x 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail: =A0=A0=A0 =A0 co= mputationalboy(at)gmail.com<= /a>




--
Esther Sala Arg=FCello,= PhD student.
Nutrigenomics Research Group
Biochemistry & Biotech= nology Department
Universitat Rovira i Virgili
Lab 111
Phone +34 9= 77558486
C/Marcel=B7l=ED Domingo s/n
43007
Tarragona (Catalonia, Spain)
--00163625717542c16404856f9277-- From owner-chemistry@ccl.net Fri Apr 30 09:52:00 2010 From: "Gerard Pujadas gerard.pujadas__gmail.com" To: CCL Subject: CCL: Software for 2D to 3D conversion that removes molecules that have (at least) one chiral center with unknown stereochemistry Message-Id: <-41762-100430042654-12524-4gWRgmCBOB/1Vwmj+bPcIA||server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0015174c3e845d372f04856f91bb Date: Fri, 30 Apr 2010 09:55:33 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas]~[gmail.com] --0015174c3e845d372f04856f91bb Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL list members, we have an sdf file where the ligands are in 2D and we would like to conver= t it onto 3D structures. Moreover, during that process we would like to remov= e all the ligands that have unknown chirality of at least one chiral center (in other words, we want to build one stereochemistry unambiguous 3D database). Reading the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we could made a simply PERL script that looks for all the molecules that have at least one bond with the label " 4" at the 10-12 column of the bond block. Unfortunately this seems to be no possible because the sdf file that we want to use as input (obtained from Reaxys) does not include this " 4" label (or not always include it) to indicate unknown chirality. For instance, the next molecule has two chiral centers with unknown chirality but nothing in the sdf annotation is telling this: Reaxys_1162 HDR 7 7 0 0 0 0 0 0 0 0999 V2000 0.9496 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7604 1.5381 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1.2585 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5682 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2594 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 3.5208 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 2 5 1 0 0 0 0 3 6 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 M REG 1162 M END We use LigPrep (Schr=F6dinger) for 2D to 3D conversion of ligand sdf files but, at present, it cannot remove molecules that have (at least) one chiral center with unknown stereochemistry during such conversion. Thus, I wonder if there is any program (either in graphical or command-line mode) that can do that (at this point it is important to remember that the existence of a chiral center has to be searched by the software at the moment of building the 3D structure because the SDF file does not mention the existence of chiral centers with unknown chirality). If you need more information about this question or something is not clear for you, please do not hesitate to write me With many thanks in advances Yours sincerely Gerard --=20 Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22 Nutrigenomics Research Group Biochemistry and Biotechnology Department Universitat Rovira i Virgili Tarragona, Catalonia --0015174c3e845d372f04856f91bb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL list members,

we have an sdf file where the ligands are in 2D and we would like to convert it onto 3D structures. Moreover, during that process we would like to remove all the ligands that have unknown chirality of at least one chiral center (in other words, we want to build one stereochemistry unambiguous 3D database). Reading the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we could made a simply PERL script that looks for all the molecules that have at least one bond with the label "=A0 4" = at the 10-12 column of the bond block. Unfortunately this seems to be no possible because the sdf file that we want to use as input (obtained > from Reaxys) does not include this "=A0 4" label (or not always i= nclude it) to indicate unknown chirality. For instance, the next molecule has two = chiral centers with unknown chirality but nothing in the sdf annotation is telling this:
Reaxys_1162

HDR
=A0 7=A0 7=A0 = 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0999 V2000
=A0=A0=A0 0.9496=A0=A0=A0 = 0.9496=A0=A0=A0 0.0000 C=A0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0= 0=A0 0=A0 0
=A0=A0=A0 1.7604=A0=A0=A0 1.5381=A0=A0=A0 0.0000 S=A0=A0 0=A0 0=A0 0=A0 0= =A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0
=A0=A0=A0 1.2585=A0=A0=A0 0.000= 0=A0=A0=A0 0.0000 S=A0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0= 0=A0 0
=A0=A0=A0 0.0000=A0=A0=A0 1.2595=A0=A0=A0 0.0000 C=A0=A0 0=A0 0= =A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0
=A0=A0=A0 2.5682=A0= =A0=A0 0.9496=A0=A0=A0 0.0000 C=A0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0= =A0 0=A0 0=A0 0=A0 0
=A0=A0=A0 2.2594=A0=A0=A0 0.0000=A0=A0=A0 0.0000 S=A0=A0 0=A0 0=A0 0=A0 0= =A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0
=A0=A0=A0 3.5208=A0=A0=A0 1.259= 5=A0=A0=A0 0.0000 C=A0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0 0=A0= 0=A0 0
=A0 1=A0 2=A0 1=A0 0=A0 0=A0 0=A0 0
=A0 1=A0 3=A0 1=A0 0=A0 0= =A0 0=A0 0
=A0 1=A0 4=A0 1=A0 0=A0 0=A0 0=A0 0
=A0 2=A0 5=A0 1=A0 0=A0 0=A0 0=A0 0
=A0 3=A0 6=A0 1=A0 0=A0 0=A0 0=A0 0<= br>=A0 5=A0 6=A0 1=A0 0=A0 0=A0 0=A0 0
=A0 5=A0 7=A0 1=A0 0=A0 0=A0 0=A0= 0
M=A0 REG 1162
M=A0 END

We use LigPrep (Schr=F6dinger)= for 2D to 3D conversion of ligand sdf files but, at present, it cannot rem= ove molecules that have (at least) one chiral center with unknown stereoche= mistry during such conversion.

Thus, I wonder if there is any program (either in graphical or command-= line mode) that can do that (at this point it is important to remember that= the existence of a chiral center has to be searched by the software at the= moment of building the 3D structure because the SDF file does not mention = the existence of chiral centers with unknown chirality).

If you need more information about this question or something is not cl= ear for you, please do not hesitate to write me

With many thanks in = advances

Yours sincerely

Gerard


--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fi= txa.jsp?id=3D22
Nutrigenomics Research Group
Biochemistry and Bio= technology Department
Universitat Rovira i Virgili
Tarragona, Catalonia
--0015174c3e845d372f04856f91bb-- From owner-chemistry@ccl.net Fri Apr 30 10:27:01 2010 From: "=?iso-8859-1?Q?Jordi_Vill=E0?= jordi.villafreixa---gmail.com" To: CCL Subject: CCL: how I can model for a protein homology? Message-Id: <-41763-100430020903-15656-sZ0aopmznGkSL1n5yRqRYg * server.ccl.net> X-Original-From: =?iso-8859-1?Q?Jordi_Vill=E0?= Content-Type: multipart/alternative; boundary=Apple-Mail-12-91506739 Date: Fri, 30 Apr 2010 07:06:06 +0200 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: =?iso-8859-1?Q?Jordi_Vill=E0?= [jordi.villafreixa#%#gmail.com] --Apple-Mail-12-91506739 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 check=20 ,ARTICLE{Centeno2003a,=20 author =3D {NB Centeno and J Vill{\`a}-Freixa and B Oliva},=20 title =3D {Teaching structural bioinformatics at the undergraduate = level},=20 journal =3D {Biochem. Mol. Biol. Educ},=20 year =3D {2003},=20 volume =3D {31},=20 pages =3D {386--391} } On Apr 29, 2010, at 6:47 PM, Naudis Antonio De Voz = ndev{:}unicartagena.edu.co wrote: >=20 > Sent to CCL by: "Naudis Antonio De Voz" [ndev^unicartagena.edu.co] > is that I've been reading about by homology modeling proteins , but I = could not find a clear methodology ... and I really want to know how to = build a theoretical model, since I need one for a study... thanks very = much >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 ---- Jordi Vill=E0 i Freixa CBBL at Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biom=E8dica de Barcelona C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: jvilla,imim.es // http://cbbl.imim.es=20 --Apple-Mail-12-91506739 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1

Sent to CCL by: "Naudis Antonio De Voz" = [ndev^unicartagena.edu.co]
is that I've been reading about by = homology modeling proteins , but I could not find a clear methodology = ... and I really want to know how to build a theoretical model, since I = need one for a study... thanks very much



-=3D This is = automatically added to each message by the mailing script =3D-
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
look up the X-Original-From: line in the mail = header.

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<= /div>
----
Jordi Vill=E0 i Freixa
CBBL = at Research Group on Biomedical Informatics (GRIB) - = IMIM/UPF
Parc de Recerca Biom=E8dica de Barcelona
C/ Doctor = Aiguader, 88; 08003 Barcelona (Spain)
Tel: +34 93 316 0504 // Fax: = +34 93 316 0550
e-mail: jvilla,imim.es // http://cbbl.imim.es 

= --Apple-Mail-12-91506739-- From owner-chemistry@ccl.net Fri Apr 30 11:02:00 2010 From: "David Watson dewatson-#-olemiss.edu" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41764-100430001720-30312-iYojhSRCLxzS1BfyIEW5/Q**server.ccl.net> X-Original-From: David Watson Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Thu, 29 Apr 2010 23:16:53 -0500 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: David Watson [dewatson*|*olemiss.edu] On Apr 29, 2010, at 3:03 PM, Igor Filippov Contr = filippovi_._mail.nih.gov wrote: >=20 > Sent to CCL by: "Igor Filippov [Contr]" [filippovi*|*mail.nih.gov] > Just saw it today -=20 >=20 > = http://infoworld.com/d/mobilize/infoworld-review-free-remote-access-tools-= windows-and-mac-018 >=20 > Igor >=20 > P.S. Not sure what kind of work would require gigabit ethernet. I'm > connecting using Remote Desktop from home. Works fine over 2Mbps (or > whatever Comcast is letting me use this days). > I wouldn't recommend 3D graphics over the net though of course. I was referring specifically to "running 3D graphics such as PyMOL", a = la: >>>=20 >>> Has anybody successfully used remote desktop software from a Mac = (Snow Leopard) to a headless PC (Windows XP or 7), especially for = running 3D graphics such as PyMOL? While I am a mac-o-phile, there are = various programs that aren't available that I am interested in. There = are also a lot of interesting little machines appearing (Nvidia ION = desktops, etc). If I could have the machine and not have to worry about = KVM switching, that would be a win. >>=20 >>=20 >>> What software did you use, and did it work over WIFi or was a cable = connection required? Inquiring minds want to know! >>>=20 I have used PyMOL in this sort of fashion on Vista to Mac OS X, and = Xwindows tunneled over ssh from Linux to Mac, both over Gigabit = ethernet. I would regard it as too slow to do the things the original poster = wanted to perform, such as "running 3D graphics such as PyMOL". (see = above) >>=20 >> You won't be able to do modeling without a high speed connection. >> Gigabit ethernet is the way to go, unless by some magical chance you = have a fiber network card in your mac and a fiber switch in your lab. >> Of course you can remotely log-in over wireless, but I think you will = soon tire of the time it takes to get any work accomplished. >>=20 For work that merely required computational effort, such as running MOE = or Sybyl, then the speed of the connection doesn't matter at all. But you can always run PyMOL, MOE or Sybyl on Mac OS X, so ???? Perhaps running quantum chemistry packages such as Firefly would benefit = > from running natively under Windows? From owner-chemistry@ccl.net Fri Apr 30 11:37:01 2010 From: "Pedro Silva pedros**ufp.edu.pt" To: CCL Subject: CCL: Protein structure prediction through fold recognition Message-Id: <-41765-100430053005-13797-4QDIMzy0U5mzk0ei7W94hQ,+,server.ccl.net> X-Original-From: Pedro Silva Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 30 Apr 2010 09:33:06 +0100 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros|a|ufp.edu.pt] In some difficult cases, hydrophobic cluster analysis may allow the detection of faint homologies. A program that compares your query sequence to every member of PDB90 is available in http://www2.ufp.pt/~pedros/HCA_db/downloads.htm. The relevant link on that page is the one to "Automated comparisons vs. PDB= 90." Further background is available in Silva, P.J. (2007) "Assessing the reliability of sequence similarities detected through hydrophobic sequence analysis" Proteins: Structure, Function and Bioinformatics, 70, 1588-1594. Good luck! Pedro On Thu, Apr 29, 2010 at 2:48 PM, Jian Wang computationalboy . gmail.com wrote: > > Dear all: > Can anyone recommend some program for protein fold recognition from a > primary sequence? > I can not find good homology protein for my target sequence. > Thanks in advance! > > -- > Jian Wang (Arthur) > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: =A0=A0=A0 =A0 computationalboy(at)gmail.com > > --=20 Pedro J. Silva Assistant Professor Universidade Fernando Pessoa Porto - Portugal http://www2.ufp.pt/~pedros/science/science.htm From owner-chemistry@ccl.net Fri Apr 30 12:11:01 2010 From: "Ellen Peeters ellen.peeters+/-student.uhasselt.be" To: CCL Subject: CCL:G: Problem with MP2 Message-Id: <-41766-100430093849-14032-MKqyVDvBb2Ze/bMvKgkMDw|,|server.ccl.net> X-Original-From: "Ellen Peeters" Date: Fri, 30 Apr 2010 09:38:48 -0400 Sent to CCL by: "Ellen Peeters" [ellen.peeters|*|student.uhasselt.be] Hello, I'm having trouble calculating an ion with MP2=Full, cc-pVTZ basis set. I entered Opt=Tight and increased the MW to %Mem=400 MW. The problem is that i'm still getting an error with l906: Not enough memory for MaxTyp=4 IDeriv=1: MinMDV= 9246618 but MDV= 6259850. Error termination via Lnk1e in /Applications/g03/l906.exe at Thu Apr 29 15:30:25 2010. It is a simple ion with one V and two O atoms. Could someone please help me? Thank you very much, with kind regards Ellen From owner-chemistry@ccl.net Fri Apr 30 12:46:00 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600*o*gmail.com" To: CCL Subject: CCL:G: MP2 failure Message-Id: <-41767-100430112037-16821-g1wi6jzsjRKIgN5AsQeazA%%server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=00032555b16a43762c048575c8db Date: Fri, 30 Apr 2010 10:20:24 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600]![gmail.com] --00032555b16a43762c048575c8db Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you: Xunlei, Soren, and Heath! I obtained the optimized structures right now. I am trying to fix the frequency problem by increasing my hardware resources. Best. Jane 2010/4/29 Heath Watts hdw115*|*psu.edu > Hi Jane, > Try using more MaxDisk space, more processors, and more memory. If your > frequency job stops (assuming you're using Gaussian 03), the job will hav= e > to restart from the beginning, because MP2 calculates frequencies > analytically rather than numerically; therefore, if the job stops, it won= 't > restart from the last freq calculation step.If you are using G09, you can > restart a frequency calculation. Our group was recently working on a 51-a= tom > model showing the intermolecular interaction between an amino acid and a > monosaccharide. Using MP2/6-31(d), the job kept dying when we tried to ru= n > it with 16 processors, 8GB or memory, and MaxDisk=3D8GB. We were ultimate= ly > able to do the calculation in just three days using 32 processors, 128GB = or > memory, and MaxDisk=3D500GB. I think that the calculation was finally > successful due to the amount of MaxDisk and memory that we were able to > allocate to the job. MP2 makes some very large checkpoint and temporary > files when it does frequency calculations, so it needs plenty of MaxDisk > space. Good luck. > Best, > Heath > > 2010/4/29 =E6=AE=B7=E5=81=A5 janeyin600_._gmail.com > > Hi there, >> >> I have some trouble with calculating some MP2 jobs recently. I found >> that the combination of "opt freq" will automatically generate a link af= ter >> the energy has converged: >> >> Normal termination of Gaussian 03 at Wed Apr 28 06:22:56 2010. >> Link1: Proceeding to internal job step number 2. >> -------------------------------------------------------------------- >> #N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G(d) F= req >> and then it will continue to run for a while. For most MP2 jobs I am now >> carrying on, it finished the first step, but failed at the second step. = I am >> now separating "freq" and "opt" commands. Don't know if that works... >> >> Any advice? Thank you very much~~ >> >> Jane >> > > --00032555b16a43762c048575c8db Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thank you: Xunlei, Soren, and Heath!
=C2=A0
I obtained the optimized structures right now. I am trying to fix the = frequency problem by increasing=C2=A0my hardware resources.
=C2=A0
Best.
Jane=C2=A0

2010/4/29 Heath Watts hdw115*|*psu.edu <owner-chemistry:ccl.net>
Hi Jane,
Try using more MaxDi= sk space, more processors, and more memory. If your frequency job stops (as= suming you're using Gaussian 03), the job will have to restart from the= beginning, because MP2 calculates frequencies analytically rather than num= erically; therefore, if the job stops, it won't restart from the last f= req calculation step.If you are using G09, you can restart a frequency calc= ulation. Our group was recently working on a 51-atom model showing the inte= rmolecular interaction between an amino acid and a monosaccharide. Using MP= 2/6-31(d), the job kept dying when we tried to run it with 16 processors, 8= GB or memory, and MaxDisk=3D8GB. We were ultimately able to do the calculat= ion in just three days using 32 processors, 128GB or memory, and MaxDisk=3D= 500GB. I think that the calculation was finally successful due to the amoun= t of MaxDisk and memory that we were able to allocate to the job. MP2 makes= some very large checkpoint and temporary files when it does frequency calc= ulations, so it needs plenty of MaxDisk space. Good luck.
Best,
Heath

2010/4/29 =E6=AE=B7=E5=81=A5 janeyin600_._gmail.com &= lt;owner-ch= emistry=C3=8Cl.net>=20

Hi there,
=C2=A0
I have some trouble wi= th calculating=C2=A0some MP2=C2=A0jobs recently. I=C2=A0found that=C2=A0the= combination of "opt=C2=A0freq" will=C2=A0automatically generate= =C2=A0a link after the energy has converged:
=C2=A0
=C2=A0Normal termi= nation of Gaussian 03 at Wed Apr 28 06:22:56 2010.
=C2=A0Link1:=C2=A0 Pr= oceeding to internal job step number=C2=A0 2.
=C2=A0--------------------------------------------------------------------<= br>=C2=A0#N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G= (d) Freq
and then it will= continue to run for a while. For most=C2=A0MP2 jobs I am now carrying on, = it finished the first step, but failed at the second step. I am now separat= ing "freq" and "opt" commands. Don't know if that w= orks...
=C2=A0
Any advice? Thank you very= much~~
=C2=A0
Jane


--00032555b16a43762c048575c8db-- From owner-chemistry@ccl.net Fri Apr 30 15:18:00 2010 From: "Igor Filippov Contr filippovi^mail.nih.gov" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41768-100430121320-3699-E0q8qCdrFQFobsmUgWleHQ(0)server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 30 Apr 2010 12:07:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [filippovi[A]mail.nih.gov] > > I have used PyMOL in this sort of fashion on Vista to Mac OS X, and Xwindows tunneled over ssh from Linux to Mac, both over Gigabit ethernet. > I would regard it as too slow to do the things the original poster wanted to perform, such as "running 3D graphics such as PyMOL". (see above) > > >> > >> You00026bcd-0010e to do modeling without a high speed connection. > >> Gigabit ethernet is the way to go, unless by some magical chance you have a fiber network card in your mac and a fiber switch in your lab. > >> Of course you can remotely log-in over wireless, but I think you will soon tire of the time it takes to get any work accomplished. > >> > > For work that merely required computational effort, such as running MOE or Sybyl, then the speed of the connection doesn't matter at all. > But you can always run PyMOL, MOE or Sybyl on Mac OS X, so ???? > I agree 100%. I used Remote Desktop to run things like PASS and Pipeline Pilot on windows (from Linux). It worked fine for me, even with low bandwidth connection. Igor From owner-chemistry@ccl.net Fri Apr 30 15:53:00 2010 From: "Jonathan Brecher jsb:-:cambridgesoft.com" To: CCL Subject: CCL: Software for 2D to 3D conversion that removes molecules that have (at least) one chiral center with unknown stereochemistry Message-Id: <-41769-100430140957-29827-U3MnvKgIE5kfDo/sgxV0zQ[*]server.ccl.net> X-Original-From: Jonathan Brecher Content-Type: multipart/alternative; boundary="_NextPart_1_00tmd8gejQgjjfbfvVDsnWdceIJ" Date: Fri, 30 Apr 2010 13:39:29 -0400 Mime-Version: 1.0 Sent to CCL by: Jonathan Brecher [jsb|,|cambridgesoft.com] This is a multi part MIME message. --_NextPart_1_00tmd8gejQgjjfbfvVDsnWdceIJ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable At 3:55 AM -0400 4/30/10, Gerard Pujadas gerard.pujadas__gmail.com wrote: >Dear CCL list members, > >we have an sdf file where the ligands are in 2D and we would like to=20 >convert it onto 3D structures. Moreover, during that process we=20 >would like to remove all the ligands that have unknown chirality of=20 >at least one chiral center (in other words, we want to build one=20 >stereochemistry unambiguous 3D database). Reading the description of=20 >the SDF format at=20 >http://www.symyx.c= om/downloads/public/ctfile/ctfile.pdf=20 >we though that we could made a simply PERL script that looks for all=20 >the molecules that have at least one bond with the label " 4" at=20 >the 10-12 column of the bond block. Unfortunately this seems to be=20 >no possible because the sdf file that we want to use as input=20 >(obtained > from Reaxys) does not include this " 4" label (or not=20 >always include it) to indicate unknown chirality. Unfortunately, this *is* impossible to do with a simple PERL script,=20 but not for the reason you describe. Consider the following two=20 compounds: 1,4,7-trifluoroheptane FCCCC(F)CCCF 1-bromo-4,7-difluoroheptane FCCCC(F)CCCBr The first compound is achiral. It always has known chirality=20 ("none"), no matter what is stored in the SDfile. The second compound is chiral. It might have known chirality, or it=20 might have unknown chirality, for example depending on the=20 presence/absence of appropriate wedged bonds. PERL alone can't identify one compound from the other. You need to=20 perform full chemical perception, including full symmetry perception,=20 before you can find out for sure which centers are capable of=20 chirality. Once you have found out which centers are capable, only=20 then can you figure out which centers are lacking. Most cheminformatics toolkits can perform the sort of stereochemical=20 analyses that you are looking for. I happen to think that the tools=20 > from CambridgeSoft provide the most accurate answers in this area...=20 although there's a slight chance that I might be a bit biased... :-} Jonathan Brecher CambridgeSoft Corporation jsb##cambridgesoft.com --_NextPart_1_00tmd8gejQgjjfbfvVDsnWdceIJ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Re: CCL: Software for 2D to 3D conversion that =20 removes m
At 3:55 AM -0400 4/30/10, Gerard Pujadas gerard.pujadas__gmail.com wrote:
Dear CCL list members,

we have an sdf file where the ligands are in 2D and we would like to convert it onto 3D structures. Moreover, during that process we would like to remove all the ligands that have unknown chirality of at least one chiral center (in other words, we want to build one stereochemistry unambiguous 3D database). Reading the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we could made a simply PERL script that looks for all the molecules that have at least one bond with the label "  4" at the 10-12 column of the bond block. Unfortunately this seems to be no possible because the sdf file that we want to use as input (obtained > from Reaxys) does not include this "  4" label (or not always include it) to indicate unknown chirality.

Unfortunately, this *is* impossible to do with a simple PERL script, but not for the reason you describe.  Consider the following two compounds:

1,4,7-trifluoroheptane
FCCCC(F)CCCF

1-bromo-4,7-difluoroheptane
FCCCC(F)CCCBr

The first compound is achiral.  It always has known chirality ("none"), no matter what is stored in the SDfile.

The second compound is chiral.  It might have known chirality, or it might have unknown chirality, for example depending on the presence/absence of appropriate wedged bonds.

PERL alone can't identify one compound from the other.  You need to perform full chemical perception, including full symmetry perception, before you can find out for sure which centers are capable of chirality.  Once you have found out which centers are capable, only then can you figure out which centers are lacking.

Most cheminformatics toolkits can perform the sort of stereochemical analyses that you are looking for.  I happen to think that the tools from CambridgeSoft provide the most accurate answers in this area... although there's a slight chance that I might be a bit biased... :-}


Jonathan Brecher
CambridgeSoft Corporation
jsb##cambridgesoft.com
--_NextPart_1_00tmd8gejQgjjfbfvVDsnWdceIJ-- From owner-chemistry@ccl.net Fri Apr 30 16:28:01 2010 From: "Greg Warren greg ~~ eyesopen.com" To: CCL Subject: CCL: Software for 2D to 3D conversion that removes molecules that have (at least) one chiral center with unknown stereochemistry Message-Id: <-41770-100430115910-22176-ww3Y/YDiW707xdxzrmwppw*o*server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_BB3CCF2D3D6B094D96588383620C5F3E4E6532C0B1EXVMBX01811ex_" Date: Fri, 30 Apr 2010 08:28:28 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg*_*eyesopen.com] --_000_BB3CCF2D3D6B094D96588383620C5F3E4E6532C0B1EXVMBX01811ex_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Gerard, The new version of Omega2 (OpenEye's conformer generator) will have exactly= the option you seek. All molecules with non-specified chiral centers will= be placed in the omega fail file and conformation(s) generated for only th= ose compounds with completely specified chiral centers. Omega reads a numb= er of 1- or 2-D molecular formats including SDF. This would give you a com= mand line solution to your problem. Unfortunately this version has not bee= n released yet - it is expected to be released before June 1. You can fil= ter you 2D data set using a small OEChem program to remove all molecules wi= th unspecified stereo centers or the functionality described for the Omega = 2.4 application is already present in the latest Omega toolkit version. Th= ese solution would require some programming and knowledge of python, java, = or C++. OpenEye provides academic licenses for all its software to academic researc= hers. These licenses are provided at no cost, but with certain conditions d= etailed in the license agreement. These conditions include validation of ac= ademic status as a research group leader (e.g. P.I.) and rules for use of o= ur software in non-academic circumstances. . Please find the appropriate ap= plication form at http://www.eyesopen.com/forms/academic_license_app.php. Since academic licenses are provided at no cost I hope this post will not t= aken as a sales pitch. Regards, Greg =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 Gregory Warren, PhD Senior Applications Scientist CEAPAS OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg:_:eyesopen.com =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 > From: owner-chemistry+greg=3D=3Deyesopen.com:_:ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com:_:ccl.net] On Behalf Of Gerard Pujadas gerard.pujada= s__gmail.com Sent: Friday, April 30, 2010 1:56 AM To: Greg Warren Subject: CCL: Software for 2D to 3D conversion that removes molecules that = have (at least) one chiral center with unknown stereochemistry Dear CCL list members, we have an sdf file where the ligands are in 2D and we would like to conver= t it onto 3D structures. Moreover, during that process we would like to rem= ove all the ligands that have unknown chirality of at least one chiral cent= er (in other words, we want to build one stereochemistry unambiguous 3D dat= abase). Reading the description of the SDF format at http://www.symyx.com/d= ownloads/public/ctfile/ctfile.pdf we though that we could made a simply PER= L script that looks for all the molecules that have at least one bond with = the label " 4" at the 10-12 column of the bond block. Unfortunately this s= eems to be no possible because the sdf file that we want to use as input (o= btained > from Reaxys) does not include this " 4" label (or not always inc= lude it) to indicate unknown chirality. For instance, the next molecule has= two chiral centers with unknown chirality but nothing in the sdf annotatio= n is telling this: Reaxys_1162 HDR 7 7 0 0 0 0 0 0 0 0999 V2000 0.9496 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7604 1.5381 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1.2585 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5682 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2594 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 3.5208 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 2 5 1 0 0 0 0 3 6 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 M REG 1162 M END We use LigPrep (Schr=F6dinger) for 2D to 3D conversion of ligand sdf files = but, at present, it cannot remove molecules that have (at least) one chiral= center with unknown stereochemistry during such conversion. Thus, I wonder if there is any program (either in graphical or command-line= mode) that can do that (at this point it is important to remember that the= existence of a chiral center has to be searched by the software at the mom= ent of building the 3D structure because the SDF file does not mention the = existence of chiral centers with unknown chirality). If you need more information about this question or something is not clear = for you, please do not hesitate to write me With many thanks in advances Yours sincerely Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22 Nutrigenomics Research Group Biochemistry and Biotechnology Department Universitat Rovira i Virgili Tarragona, Catalonia --_000_BB3CCF2D3D6B094D96588383620C5F3E4E6532C0B1EXVMBX01811ex_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Gerard,

 

The new version of Omega2 (OpenEye’s conformer generator) will have exact= ly the option you seek.=A0 All molecules with non-specified chiral centers will be placed in the omega fail file and conformation(s) generated for only those compounds with completely specified chiral centers. =A0Omega reads a number= of 1- or 2-D molecular formats including SDF. =A0This would give you a command li= ne solution to your problem.=A0 Unfortunately this version has not been releas= ed yet=A0 - it is expected to be released before June 1.=A0 You can filter you= 2D data set using a small OEChem program to remove all molecules with unspecified stereo centers or the functionality described for the Omega 2.4 application= is already present in the latest Omega toolkit version.=A0 These solution woul= d require some programming and knowledge of python, java, or C++.<= /span>

 

OpenEye provides academic licenses for all its software to academic researchers. Th= ese licenses are provided at no cost, but with certain conditions detailed in t= he license agreement. These conditions include validation of academic status a= s a research group leader (e.g. P.I.) and rules for use of our software in non-academic circumstances. . Please find the appropriate application form = at http://www.eyesopen.com/forms/academic_license_app.php.

 

Since academic licenses are provided at no cost I hope this post will not taken a= s a sales pitch.

 

Regards,

 

Greg

=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

Gregory Warren, PhD

Senior Applications Scientist

CEAPAS

OpenEye Scientific Software, Inc

9 Bisbee Court, Suite D

Santa Fe, NM 87508

(505) 473-7385 ext 50

mailto:greg:_:eyesopen.com

=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

 

 

 

From: owner-chemistry+greg=3D=3Deyesopen.com:_:ccl.net [mailto:owner-chemistry+greg=3D=3Deyesopen.com:_:ccl.net] On Behalf Of Gerard Pujadas gerard.pujadas__gmail.com
Sent: Friday, April 30, 2010 1:56 AM
To: Greg Warren
Subject: CCL: Software for 2D to 3D conversion that removes molecule= s that have (at least) one chiral center with unknown stereochemistry

 

Dear CCL list members,<= br>
we have an sdf file where the ligands are in 2D and we would like to conver= t it onto 3D structures. Moreover, during that process we would like to remove a= ll the ligands that have unknown chirality of at least one chiral center (in o= ther words, we want to build one stereochemistry unambiguous 3D database). Readi= ng the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we could made a simply PERL script that looks for all the molecules that have at least one bond with the label "  4" a= t the 10-12 column of the bond block. Unfortunately this seems to be no possi= ble because the sdf file that we want to use as input (obtained > from Reaxy= s) does not include this "  4" label (or not always include it)= to indicate unknown chirality. For instance, the next molecule has two chiral centers with unknown chirality but nothing in the sdf annotation is telling this:

Reaxys_1162

HDR
  7  7  0  0  0  0  0  0  0&nb= sp; 0999 V2000
    0.9496    0.9496    0.0000 C   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
    1.7604    1.5381    0.0000 S   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
    1.2585    0.0000    0.0000 S   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
    0.0000    1.2595    0.0000 C   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
    2.5682    0.9496    0.0000 C   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
    2.2594    0.0000    0.0000 S   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
    3.5208    1.2595    0.0000 C   0  0  0  0  0  0  0  0&nbs= p; 0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  REG 1162
M  END


We use LigPrep (Schr=F6dinger) for 2D to 3D conversion of ligand sdf files = but, at present, it cannot remove molecules that have (at least) one chiral cent= er with unknown stereochemistry during such conversion.

Thus, I wonder if there is any program (either in graphical or command-line mode) that can do that (at this point it is important to remember that the existence of a chiral center has to be searched by the software at the mome= nt of building the 3D structure because the SDF file does not mention the existence of chiral centers with unknown chirality).

If you need more information about this question or something is not clear = for you, please do not hesitate to write me

With many thanks in advances

Yours sincerely

Gerard



--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia

--_000_BB3CCF2D3D6B094D96588383620C5F3E4E6532C0B1EXVMBX01811ex_-- From owner-chemistry@ccl.net Fri Apr 30 17:03:00 2010 From: "Wolf Ihlenfeldt wdi]~[xemistry.com" To: CCL Subject: CCL: Software for 2D to 3D conversion that removes molecules that have (at least) one chiral center with unknown stereochemistry Message-Id: <-41771-100430123637-25283-/ZZR8PJ1rFaatSBWR74oTA\a/server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=0016e6497dfc40bb3d04857611ce Date: Fri, 30 Apr 2010 16:40:48 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi(~)xemistry.com] --0016e6497dfc40bb3d04857611ce Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable This is easily done with a tiny Cactvs toolkit script (www.xemistry.com, free for academic users): --- snip --- set fh [molfile open [lindex $argv 0] r hydrogens add] molfile loop $fh eh { ens need $eh A_LABEL_STEREO if {[ens atoms $eh astereogenic count]!=3D[ens atoms $eh astereo count]= } continue molfile copy $fh stdout 1 -1 } molfile close all ---- snip --- Run with the generic interpreter from the package as csts -f myscript.tcl mysdfile.sdf Records which pass the test are copied in byte-exact fashion to standard output. Of course this script is just a start, feel free to modify - for example, test also for proper bond cis/trans stereo definition On Fri, Apr 30, 2010 at 8:55 AM, Gerard Pujadas gerard.pujadas__gmail.com < owner-chemistry,+,ccl.net> wrote: > Dear CCL list members, > > we have an sdf file where the ligands are in 2D and we would like to > convert it onto 3D structures. Moreover, during that process we would lik= e > to remove all the ligands that have unknown chirality of at least one chi= ral > center (in other words, we want to build one stereochemistry unambiguous = 3D > database). Reading the description of the SDF format at > http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we > could made a simply PERL script that looks for all the molecules that hav= e > at least one bond with the label " 4" at the 10-12 column of the bond > block. Unfortunately this seems to be no possible because the sdf file th= at > we want to use as input (obtained > from Reaxys) does not include this " = 4" > label (or not always include it) to indicate unknown chirality. For > instance, the next molecule has two chiral centers with unknown chirality > but nothing in the sdf annotation is telling this: > > Reaxys_1162 > > HDR > 7 7 0 0 0 0 0 0 0 0999 V2000 > 0.9496 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.7604 1.5381 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 1.2585 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5682 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.2594 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 3.5208 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 3 1 0 0 0 0 > 1 4 1 0 0 0 0 > 2 5 1 0 0 0 0 > 3 6 1 0 0 0 0 > 5 6 1 0 0 0 0 > 5 7 1 0 0 0 0 > M REG 1162 > M END > > We use LigPrep (Schr=C3=B6dinger) for 2D to 3D conversion of ligand sdf f= iles > but, at present, it cannot remove molecules that have (at least) one chir= al > center with unknown stereochemistry during such conversion. > > Thus, I wonder if there is any program (either in graphical or command-li= ne > mode) that can do that (at this point it is important to remember that th= e > existence of a chiral center has to be searched by the software at the > moment of building the 3D structure because the SDF file does not mention > the existence of chiral centers with unknown chirality). > > If you need more information about this question or something is not clea= r > for you, please do not hesitate to write me > > With many thanks in advances > > Yours sincerely > > Gerard > > > > -- > Gerard Pujadas > http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22 > Nutrigenomics Research Group > Biochemistry and Biotechnology Department > Universitat Rovira i Virgili > Tarragona, Catalonia > --0016e6497dfc40bb3d04857611ce Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
This is easily done with a tiny Cactvs toolkit script (www.xemistry.com, free for academic users):

= --- snip ---
set fh [molfile open [lindex $argv 0] r hydrogens add]
molfile loop $fh eh {
=C2=A0=C2=A0=C2=A0 ens need $eh A_LABEL_STEREO
= =C2=A0=C2=A0=C2=A0 if {[ens atoms $eh astereogenic count]!=3D[ens atoms $eh= astereo count]} continue
=C2=A0=C2=A0=C2=A0 molfile copy $fh stdout 1 -= 1
}
molfile close all
---- snip ---

Run with the generic interpreter from the package as

csts -f my= script.tcl mysdfile.sdf

Records which pass the test are copied in by= te-exact fashion to standard output.

Of course this script is just = a start, feel free to modify - for example,=C2=A0 test also for proper bond= cis/trans stereo definition



On Fri, Apr 30, 2010 at 8:55 AM, Ger= ard Pujadas gerard.pujadas__gm= ail.com <owner-chemistry,+,ccl.net> wrote:
Dear CCL list mem= bers,

we have an sdf file where the ligands are in 2D and we would like to convert it onto 3D structures. Moreover, during that process we would like to remove all the ligands that have unknown chirality of at least one chiral center (in other words, we want to build one stereochemistry unambiguous 3D database). Reading the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we could made a simply PERL script that looks for all the molecules that have at least one bond with the label "=C2=A0 4&quo= t; at the 10-12 column of the bond block. Unfortunately this seems to be no possible because the sdf file that we want to use as input (obtained > from Reaxys) does not include this "=C2=A0 4" label (or not = always include it) to indicate unknown chirality. For instance, the next molecule has two = chiral centers with unknown chirality but nothing in the sdf annotation is telling this:
Reaxys_1162

HDR
=C2=A0 7=C2=A0= 7=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0999 V2000=
=C2=A0=C2=A0=C2=A0 0.9496=C2=A0=C2=A0=C2=A0 0.9496=C2=A0=C2=A0=C2=A0 0.= 0000 C=C2=A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 = 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0=C2=A0=C2=A0 1.7604=C2=A0=C2=A0=C2=A0 1.5381=C2=A0=C2=A0=C2=A0 0.0000= S=C2=A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2= =A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0=C2=A0=C2=A0 1.2585=C2=A0=C2=A0=C2= =A0 0.0000=C2=A0=C2=A0=C2=A0 0.0000 S=C2=A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0= =C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0= =C2=A0=C2=A0 0.0000=C2=A0=C2=A0=C2=A0 1.2595=C2=A0=C2=A0=C2=A0 0.0000 C=C2= =A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0= =C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0=C2=A0=C2=A0 2.5682=C2=A0=C2=A0=C2=A0 0.9= 496=C2=A0=C2=A0=C2=A0 0.0000 C=C2=A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 = 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0=C2=A0=C2=A0 2.2594=C2=A0=C2=A0=C2=A0 0.0000=C2=A0=C2=A0=C2=A0 0.0000= S=C2=A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2= =A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0=C2=A0=C2=A0 3.5208=C2=A0=C2=A0=C2= =A0 1.2595=C2=A0=C2=A0=C2=A0 0.0000 C=C2=A0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0= =C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0 = 1=C2=A0 2=C2=A0 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0 1=C2=A0 3=C2=A0= 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0 1=C2=A0 4=C2=A0 1=C2=A0 0=C2= =A0 0=C2=A0 0=C2=A0 0
=C2=A0 2=C2=A0 5=C2=A0 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0 3=C2=A0 = 6=C2=A0 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0 5=C2=A0 6=C2=A0 1=C2=A0= 0=C2=A0 0=C2=A0 0=C2=A0 0
=C2=A0 5=C2=A0 7=C2=A0 1=C2=A0 0=C2=A0 0=C2= =A0 0=C2=A0 0
M=C2=A0 REG 1162
M=C2=A0 END

We use LigPre= p (Schr=C3=B6dinger) for 2D to 3D conversion of ligand sdf files but, at pr= esent, it cannot remove molecules that have (at least) one chiral center wi= th unknown stereochemistry during such conversion.

Thus, I wonder if there is any program (either in graphical or command-= line mode) that can do that (at this point it is important to remember that= the existence of a chiral center has to be searched by the software at the= moment of building the 3D structure because the SDF file does not mention = the existence of chiral centers with unknown chirality).

If you need more information about this question or something is not cl= ear for you, please do not hesitate to write me

With many thanks in = advances

Yours sincerely

Gerard



--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fi= txa.jsp?id=3D22
Nutrigenomics Research Group
Biochemistry and Bio= technology Department
Universitat Rovira i Virgili
Tarragona, Catalonia

--0016e6497dfc40bb3d04857611ce-- From owner-chemistry@ccl.net Fri Apr 30 17:38:00 2010 From: "Ramachandran Chelat rcchelat!^!rediffmail.com" To: CCL Subject: CCL: Qchem frequency output visualization Message-Id: <-41772-100430151427-8398-E0q8qCdrFQFobsmUgWleHQ .. server.ccl.net> X-Original-From: "Ramachandran Chelat" Date: Fri, 30 Apr 2010 15:14:25 -0400 Sent to CCL by: "Ramachandran Chelat" [rcchelat#rediffmail.com] Dear CCL friends, Could you tell me a freely available visualization software to view the frequency output of Qchem calculations? I could see the optimized geometry using molden. But frequency icon is not active for the same. Thanking you, Ramachandran From owner-chemistry@ccl.net Fri Apr 30 18:51:00 2010 From: "David Watson dewatson-x-olemiss.edu" To: CCL Subject: CCL: Qchem frequency output visualization Message-Id: <-41773-100430184721-4463-6wKlPeCehOBljORFADvong]*[server.ccl.net> X-Original-From: David Watson Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Fri, 30 Apr 2010 17:47:07 -0500 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: David Watson [dewatson++olemiss.edu] I see from the GAMESS list that you are using GAMESS to calculate = vibrational frequencies. You can use the program wxMacMolPlt (it will work on Windows, Linux, or = Mac) to visualize these frequencies. This is probably the optimal solution since it was designed with GAMESS = in mind. On Apr 30, 2010, at 2:14 PM, Ramachandran Chelat = rcchelat!^!rediffmail.com wrote: >=20 > Sent to CCL by: "Ramachandran Chelat" [rcchelat#rediffmail.com] > Dear CCL friends, > Could you tell me a freely available visualization software to view = the frequency output of Qchem calculations? > I could see the optimized geometry using molden. > But frequency icon is not active for the same. >=20 > Thanking you, > Ramachandran From owner-chemistry@ccl.net Fri Apr 30 19:26:00 2010 From: "Jamin Krinsky jamink%%berkeley.edu" To: CCL Subject: CCL: Qchem frequency output visualization Message-Id: <-41774-100430185302-7050-djpA+acKU4skj8alUb10wA~~server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 30 Apr 2010 15:52:53 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink(_)berkeley.edu] Hi Ramachandran, I've found Gabedit, available free from Sourceforge, to work well for this. It's available for most platforms. Jamin On Fri, Apr 30, 2010 at 12:14 PM, Ramachandran Chelat rcchelat!^!rediffmail.com wrote: > > Sent to CCL by: "Ramachandran =A0Chelat" [rcchelat#rediffmail.com] > Dear CCL friends, > Could you tell me a freely available visualization software to view the f= requency output of Qchem calculations? > I could see the optimized geometry using molden. > But frequency icon is not active for the same. > > Thanking you, > Ramachandran > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink++berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Fri Apr 30 22:15:00 2010 From: "Andrew Orry andy]^[molsoft.com" To: CCL Subject: CCL: Software for 2D to 3D conversion that removes molecules that have (at least) one chiral center with unknown stereochemistry Message-Id: <-41775-100430132415-4883-EbHVymuh/WfVbFbFLvF5IQ]-[server.ccl.net> X-Original-From: Andrew Orry Content-Type: multipart/alternative; boundary="------------010400020102010608040409" Date: Fri, 30 Apr 2010 09:28:33 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy+/-molsoft.com] This is a multi-part message in MIME format. --------------010400020102010608040409 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Gerard, ICM-Chemist can do this http://www.molsoft.com/icm-chemist.html . We do not rely on the label in the SDF file to determine stereochemistry just the coordinates and bonds. ICM-Chemist can filter chiral centers based on "left", "right", or racemic via the command line or in the graphical user interface. Please let me know if you need more information. Thanks, Andy -- Andrew Orry Ph.D. Senior Research Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla CA 92037 Tel: 858-625-2000 x108 Fax: 828-625-2888 On 4/30/2010 12:55 AM, Gerard Pujadas gerard.pujadas__gmail.com wrote: > Dear CCL list members, > > we have an sdf file where the ligands are in 2D and we would like to > convert it onto 3D structures. Moreover, during that process we would > like to remove all the ligands that have unknown chirality of at least > one chiral center (in other words, we want to build one > stereochemistry unambiguous 3D database). Reading the description of > the SDF format at > http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that > we could made a simply PERL script that looks for all the molecules > that have at least one bond with the label " 4" at the 10-12 column > of the bond block. Unfortunately this seems to be no possible because > the sdf file that we want to use as input (obtained > from Reaxys) > does not include this " 4" label (or not always include it) to > indicate unknown chirality. For instance, the next molecule has two > chiral centers with unknown chirality but nothing in the sdf > annotation is telling this: > > Reaxys_1162 > > HDR > 7 7 0 0 0 0 0 0 0 0999 V2000 > 0.9496 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.7604 1.5381 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 1.2585 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5682 0.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.2594 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 3.5208 1.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 3 1 0 0 0 0 > 1 4 1 0 0 0 0 > 2 5 1 0 0 0 0 > 3 6 1 0 0 0 0 > 5 6 1 0 0 0 0 > 5 7 1 0 0 0 0 > M REG 1162 > M END > > We use LigPrep (Schrödinger) for 2D to 3D conversion of ligand sdf > files but, at present, it cannot remove molecules that have (at least) > one chiral center with unknown stereochemistry during such conversion. > > Thus, I wonder if there is any program (either in graphical or > command-line mode) that can do that (at this point it is important to > remember that the existence of a chiral center has to be searched by > the software at the moment of building the 3D structure because the > SDF file does not mention the existence of chiral centers with unknown > chirality). > > If you need more information about this question or something is not > clear for you, please do not hesitate to write me > > With many thanks in advances > > Yours sincerely > > Gerard > > > > -- > Gerard Pujadas > http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 > Nutrigenomics Research Group > Biochemistry and Biotechnology Department > Universitat Rovira i Virgili > Tarragona, Catalonia --------------010400020102010608040409 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Gerard,
ICM-Chemist can do this http://www.molsoft.com/icm-chemist.html . We do not rely on the label in the SDF file to determine stereochemistry just the coordinates and bonds. ICM-Chemist can filter chiral centers based on "left", "right", or racemic via the command line or in the graphical user interface. Please let me know if you need more information.
Thanks,
Andy
-- 
Andrew Orry Ph.D.
Senior Research Scientist
MolSoft LLC
3366 North Torrey Pines Court 
Suite 300
La Jolla
CA 92037
Tel: 858-625-2000 x108
Fax: 828-625-2888


On 4/30/2010 12:55 AM, Gerard Pujadas gerard.pujadas__gmail.com wrote:
Dear CCL list members,

we have an sdf file where the ligands are in 2D and we would like to convert it onto 3D structures. Moreover, during that process we would like to remove all the ligands that have unknown chirality of at least one chiral center (in other words, we want to build one stereochemistry unambiguous 3D database). Reading the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf we though that we could made a simply PERL script that looks for all the molecules that have at least one bond with the label "  4" at the 10-12 column of the bond block. Unfortunately this seems to be no possible because the sdf file that we want to use as input (obtained > from Reaxys) does not include this "  4" label (or not always include it) to indicate unknown chirality. For instance, the next molecule has two chiral centers with unknown chirality but nothing in the sdf annotation is telling this:

Reaxys_1162

HDR
  7  7  0  0  0  0  0  0  0  0999 V2000
    0.9496    0.9496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7604    1.5381    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2585    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5682    0.9496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2594    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.5208    1.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  REG 1162
M  END

We use LigPrep (Schrödinger) for 2D to 3D conversion of ligand sdf files but, at present, it cannot remove molecules that have (at least) one chiral center with unknown stereochemistry during such conversion.

Thus, I wonder if there is any program (either in graphical or command-line mode) that can do that (at this point it is important to remember that the existence of a chiral center has to be searched by the software at the moment of building the 3D structure because the SDF file does not mention the existence of chiral centers with unknown chirality).

If you need more information about this question or something is not clear for you, please do not hesitate to write me

With many thanks in advances

Yours sincerely

Gerard



--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
Nutrigenomics Research Group
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia






--------------010400020102010608040409--


From owner-chemistry@ccl.net Fri Apr 30 22:50:01 2010
From: "Ivanciuc, Ovidiu I. oiivanci#,#utmb.edu" 
To: CCL
Subject: CCL: protein homology modeling
Message-Id: <-41776-100430180954-13972-MQwEw5E67ds5F8ifYeK1aA_-_server.ccl.net>
X-Original-From: "Ivanciuc, Ovidiu I." 
Content-Language: en-US
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 30 Apr 2010 16:06:17 -0500
MIME-Version: 1.0


Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci() utmb.edu]


>>> Naudis Antonio De Voz ndev{:}unicartagena.edu.co

>>> that I've been reading about by homology modeling proteins , but I coul=
d not find a clear methodology
>>>and I really want to know how to build a theoretical model, since I need=
 one for a study... thanks very much

Here you have several pointers:

1. learn to use MODELLER=20
http://www.salilab.org/modeller/

2. as a web server, I suggest SWISS-MODEL
http://swissmodel.expasy.org/

For a good PDB template (sequence identity > 30% to the target sequence), S=
WISS-MODEL
is quite good.

3. Any homology modeling software needs as input an alignment between the t=
arget sequence
and a template structure from PDB.
This alignment is obtained from fold recognition servers:

PHYRE - http://www.sbg.bio.ic.ac.uk/servers/phyre/

mGenTHREADER - http://bioinf.cs.ucl.ac.uk/psipred/

SAM-T08 - http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html

FFAS03 - http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl

ESyPred3D - http://www.fundp.ac.be/urbm/bioinfo/esypred/

3D-JIGSAW - http://www.bmm.icnet.uk/servers/3djigsaw/

LOOPP - http://cbsuapps.tc.cornell.edu/loopp.aspx

Some of these servers offer also 3D models (PHYRE).

Several metaservers consolidate results from a selection of fold recognitio=
n servers,
thus helping to identify a best alignment:

._-_.TOME - http://abcis.cbs.cnrs.fr/AT2/meta.html

GeneSilico - https://www.genesilico.pl/meta2/

3D Jury - http://meta.bioinfo.pl/submit_wizard.pl/


4. To learn about state of the art methods in homology modeling of proteins=
, go to
CASP (Critical Assessment of protein Structure Prediction) http://predictio=
ncenter.org/
You may find there other web servers with good performance in blind predict=
ions.

CASP Proceedings are free, from http://predictioncenter.org/index.cgi?page=
=3Dproceedings

O