From owner-chemistry@ccl.net Thu Apr 27 16:36:00 2017 From: "Scott Brozell sbrozell#rci.rutgers.edu" To: CCL Subject: CCL: Announcement: Release of DOCK 6.8 Message-Id: <-52768-170427162721-13939-+M3RCC8q1ELSbOEaoIVQkA{}server.ccl.net> X-Original-From: Scott Brozell Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 27 Apr 2017 16:27:14 -0400 Mime-Version: 1.0 Sent to CCL by: Scott Brozell [sbrozell##rci.rutgers.edu] We are pleased to announce the release of DOCK 6.8. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.8 is available for download and free for academic users at http://dock.compbio.ucsf.edu/. In this release new scoring functionality is available. The pharmacophore matching similarity scoring function scores the similarity between binding candidates and known binders by matching molecular interactions based on steric and electronic features. Descriptor score enables simultaneous use of multiple scoring functions. New methods specifically implemented for this hybrid approach include Tanimoto score, Hungarian matching similarity score, and volume-based similarity score. DOCK continues to provide a variety of energy scoring functions. For full information on what is new in DOCK 6.8, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.8.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu From owner-chemistry@ccl.net Thu Apr 27 17:53:00 2017 From: "Elaine Meng meng[a]cgl.ucsf.edu" To: CCL Subject: CCL: Mol2 format specification? Message-Id: <-52769-170427164049-16313-y0Y1f4tZsaR/CSgE6Z+ZoQ]|[server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 27 Apr 2017 16:40:47 -0400 Sent to CCL by: "Elaine Meng" [meng!=!cgl.ucsf.edu] Hi folks, I can no longer find any "official" (Tripos SYBYL) Mol2 file-format description. Is anybody aware of a such a webpage or document accessible online? There isn't even a description in wikipedia, as far as I can tell. All I've found are short descriptions within the documentation for other programs. Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Thu Apr 27 20:09:00 2017 From: "Bennion, Brian bennion1(~)llnl.gov" To: CCL Subject: CCL: Mol2 format specification? Message-Id: <-52770-170427195224-27120-d13bc3mUg8HuskBwXZnnXQ~!~server.ccl.net> X-Original-From: "Bennion, Brian" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_CY1PR09MB0826A03E669F60625DD1F78BF6100CY1PR09MB0826namp_" Date: Thu, 27 Apr 2017 23:52:16 +0000 MIME-Version: 1.0 Sent to CCL by: "Bennion, Brian" [bennion1*|*llnl.gov] --_000_CY1PR09MB0826A03E669F60625DD1F78BF6100CY1PR09MB0826namp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Re: [Rdkit-discuss] official Tripos MOL2 file format PDF document Nils Weskamp Thu, 13 Apr 2017 07:48:29 -0700 Dear All, does this link help: https://www.yumpu.com/en/document/view/15425101/tripos-mol2-file-format Cheers, Nils On Thu, Apr 13, 2017 at 4:21 PM, Hannes Loeffler wrote: > On Tue, 11 Apr 2017 08:35:53 -0500 > Francois BERENGER wrote: > > > Hello, > > > > Not directly related to rdkit, but if someone that have > > the original PDF of this file format could place it > > online permanently, that would be wonderful. > > What does "permanent" mean these days? I can upload the copy I have if > you have a suggestion for a good location. > > Cheers, > Hannes. > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss(-)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ---------------------------------------------------------------------------= --- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss(-)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ________________________________ > From: Bennion, Brian Sent: Thursday, April 27, 2017 4:51:04 PM To: CCL Subscribers Subject: Re: Mol2 format specification? There was a post on the RDKIT list for this description. A user there post= ed the pdf online. I am looking for the link to share with this list. Brian Bennion ________________________________ > From: owner-chemistry+bennion1=3D=3Dllnl.gov(-)ccl.net on behalf of Elaine Meng meng[a]cgl.ucsf.edu Sent: Thursday, April 27, 2017 1:40:47 PM To: Bennion, Brian Subject: CCL: Mol2 format specification? Sent to CCL by: "Elaine Meng" [meng!=3D!cgl.ucsf.edu] Hi folks, I can no longer find any "official" (Tripos SYBYL) Mol2 file-format descrip= tion. Is anybody aware of a such a webpage or document accessible online? = There isn't even a description in wikipedia, as far as I can tell. All I'= ve found are short descriptions within the documentation for other programs= . Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_CY1PR09MB0826A03E669F60625DD1F78BF6100CY1PR09MB0826namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Re: [Rdkit-discuss] official Tripos MOL2 file form= at PDF document

Nils Weskamp Thu, 13 Apr 2017 07:48:29 -0700 

Dear All,=0A=
=0A=
does this link help:
https://www.yumpu.com/en/document/view/15425=
101/tripos-mol2-file-format=0A=
=0A=
Cheers,=0A=
Nils=0A=
=0A=
=0A=
On Thu, Apr 13, 2017 at 4:21 PM, Hannes Loeffler <hannes.loeff...(-)stfc.a=
c.uk=0A=
> wrote:=0A=
=0A=
> On Tue, 11 Apr 2017 08:35:53 -0500=0A=
> Francois BERENGER <francois.c.beren...(-)vanderbilt.edu> wrote:=0A=
>=0A=
> > Hello,=0A=
> >=0A=
> > Not directly related to rdkit, but if someone that have=0A=
> > the original PDF of this file format could place it=0A=
> > online permanently, that would be wonderful.=0A=
>=0A=
> What does "permanent" mean these days?  I can upload the cop=
y I have if=0A=
> you have a suggestion for a good location.=0A=
>=0A=
> Cheers,=0A=
> Hannes.=0A=
>=0A=
> ------------------------------------------------------------=0A=
> ------------------=0A=
> Check out the vibrant tech community on one of the world's most=0A=
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot=0A=
> _______________________________________________=0A=
> Rdkit-discuss mailing list=0A=
> Rdkit-discuss(-)lists.sourceforge.net=0A=
> https://lists.sourceforge.net/lists/listinfo/rdkit-discus=
s=0A=
>=0A=

----------------------------------------------------------------------=
--------=0A=
Check out the vibrant tech community on one of the world's most=0A=
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________=0A=
Rdkit-discuss mailing list=0A=
Rdkit-discuss(-)lists.sourceforge.net=0A=
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss=
=0A=






















































From: Bennion, Brian
Sent: Thursday, April 27, 2017 4:51:04 PM
To: CCL Subscribers
Subject: Re: Mol2 format specification?
 

There was a post on the RDKIT list for this description.  A user th= ere posted the pdf online. I am looking for the link to share with this lis= t.

Brian Bennion

From: owner-chemistry+= ;bennion1=3D=3Dllnl.gov(-)ccl.net <owner-chemistry+bennion1=3D=3Dllnl.= gov(-)ccl.net> on behalf of Elaine Meng meng[a]cgl.ucsf.edu <owner-chem= istry(-)ccl.net>
Sent: Thursday, April 27, 2017 1:40:47 PM
To: Bennion, Brian
Subject: CCL: Mol2 format specification?
 

Sent to CCL by: "Elaine  Meng" [meng!=3D!cgl.ucsf.edu]
Hi folks,
I can no longer find any "official" (Tripos SYBYL) Mol2 file-form= at description.  Is anybody aware of a such a webpage or document acce= ssible online?  There isn't even a description in wikipedia, as far as= I can tell.  All I've found are short descriptions within the documentation for other programs.
Thanks,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



-=3D This is automatically added to each message by the mailing script =3D-=       http://www.ccl.net/cgi-bin/ccl/send_ccl_message
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
      http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://w= ww.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
      =

RTFI: http:= //www.ccl.net/chemistry/aboutccl/instructions/


--_000_CY1PR09MB0826A03E669F60625DD1F78BF6100CY1PR09MB0826namp_-- From owner-chemistry@ccl.net Thu Apr 27 20:44:00 2017 From: "Cristian Bologa CBologa],[salud.unm.edu" To: CCL Subject: CCL: Mol2 format specification? Message-Id: <-52771-170427201531-31437-VvghjG1L62Emr1cfN4JKxw:_:server.ccl.net> X-Original-From: Cristian Bologa Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Apr 2017 00:15:21 +0000 MIME-Version: 1.0 Sent to CCL by: Cristian Bologa [CBologa++salud.unm.edu] Elaine, While not "official", here seems to be a copy of the the mol2 file format from the SYBYL manual. http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf Also if it has ever been available on the Tripos web site, you might be able to get it from there using the Wayback Machine http://web.archive.org/web/*/tripos.com Regards, Cristian Cristian Bologa, Ph.D. Research Professor, Div. of Translational Informatics, Dept. of Internal Medicine, Univ. of New Mexico, School of Medicine, Innovation Discovery&Training Center, MSC09 5025, 700 Camino de Salud NE, Albuquerque, NM 87131 Telephone: +1 (505) 925-7534 Fax:+1 (505) 925-7625 -----Original Message----- > From: owner-chemistry+cbologa==salud.unm.edu-*-ccl.net [mailto:owner-chemistry+cbologa==salud.unm.edu-*-ccl.net] On Behalf Of Elaine Meng meng[a]cgl.ucsf.edu Sent: Thursday, April 27, 2017 2:41 PM To: Cristian Bologa Subject: CCL: Mol2 format specification? Sent to CCL by: "Elaine Meng" [meng!=!cgl.ucsf.edu] Hi folks, I can no longer find any "official" (Tripos SYBYL) Mol2 file-format description. Is anybody aware of a such a webpage or document accessible online? There isn't even a description in wikipedia, as far as I can tell. All I've found are short descriptions within the documentation for other programs. Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Franciscohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Apr 27 21:19:00 2017 From: "Mezei, Mihaly mihaly.mezei++mssm.edu" To: CCL Subject: CCL: Mol2 format specification? Message-Id: <-52772-170427204141-7457-P/1t6ITFX5s2wxuCNkbUoQ(0)server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Apr 2017 00:41:35 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei!=!mssm.edu] > I can no longer find any "official" (Tripos SYBYL) Mol2 file-format description. Is anybody aware of a such a webpage or document accessible online? There isn't even a description in wikipedia, as far as I can tell. All I've found are short descriptions within the documentation for other programs. Have a look at http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://www.mssm.edu/departments-and-institutes/pharmacology-and-systems-therapeutics