From owner-chemistry@ccl.net Fri May 13 05:11:01 2016 From: "Igors Mihailovs igors.mihailovs0 .. gmail.com" To: CCL Subject: CCL: a really silly question Message-Id: <-52197-160513050900-26745-uyv6FEAPMCouETWAbvrL2Q**server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=94eb2c07c0b82b408c0532b59fe9 Date: Fri, 13 May 2016 12:08:25 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0:-:gmail.com] --94eb2c07c0b82b408c0532b59fe9 Content-Type: text/plain; charset=UTF-8 Dear Mr Wood, In addition to what was said by Mr Shobe, you have 3.15e-8 in your expression, while it should read 3.15e-10 (angstroem is 10^-10 m); also, charges should be multiplied not only with 10^-19, but with 1.60218e-19. With best wishes, Igors Mihailovs (engineer / PhD student) Institute of Solid State Physics University of Latvia 2016-05-12 20:56 GMT+03:00 David Shobe avidshobe_-_yahoo.com < owner-chemistry() ccl.net>: > The formula is E = (1 / 4 pi E0) (q1 q2 / r12). Thus your conversion > factor is 1 / (4 pi E0) where E0 = 8.854 187 817... x 10-12 J^-1 C^2 m-1. > Sorry for the lack of typography. > > On Thursday, May 12, 2016 10:33 AM, Richard Leo Wood rwoodphd##msn.com > wrote: > > > > Sent to CCL by: "Richard Leo Wood" [rwoodphd ~~ msn.com] > I am trying to compute the electrostatic interaction for a pair of atoms > > from an energy minimized structure. > > I have the charges on the two atoms as -0.47 and -0.55. They are 3.15 > Angstroms apart. So, E = (-0.55*-0.45)e-38 C^2/3.15e-8 m. > > I get 8.21e-32 C^2/m. My question is how do I convert this to Joules? > > Richard> ------_Part_1049358_995418990.1463075782335 > Content-Type: text/html; charsetUTF-8 > Content-Transfer-Encoding: quoted-printable > >
dir="ltr">The formula is E = (1 / 4 pi E0) (q1 q2 / r12).   Thus your > conversion factor is 1 / (4 pi E0) where E0 =  id="yui_3_16_0_ym19_1_1463074875924_34936">8.854 187 817... x 10 id="yui_3_16_0_ym19_1_1463074875924_34937">-12  J^-1 C^2 > m-1.
dir="ltr">
dir="ltr">Sorry for the lack of typography. 
class="qtdSeparateBR">

style="display: block;">
style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida > Grande, sans-serif; font-size: 16px;">
face="Arial"> On Thursday, May 12, 2016 10:33 AM, Richard Leo Wood > rwoodphd##msn.com <owner-chemistry+/-ccl.net> > wrote:



Sent to > CCL by: "Richard Leo Wood" [rwoodphd ~~ msn.com]
I am trying to > compute the electrostatic interaction for a pair of atoms
> from an > energy minimized structure.

I have the charges on the two atoms as > -0.47 and -0.55.  They are 3.15
Angstroms apart.  So, E = > (-0.55*-0.45)e-38 C^2/3.15e-8 m.

I get 8.21e-32 C^2/m.  My > question is how do I convert this to > Joules?

Richard



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Dear Mr Wood,

In addition to what was s= aid by Mr Shobe, you have 3.15e-8 in your expression, while it should read = 3.15e-10 (angstroem is 10^-10 m); also, charges should be multiplied not on= ly with 10^-19, but with 1.60218e-19.

With best wishes,
Igo= rs Mihailovs (engineer / PhD student)
Institute of Solid Stat= e Physics
University of Latvia

=

2016-05-12 20:56 GMT+03:00 David Shobe avidshobe_-_yahoo.com <owner= -chemistry() ccl.net>:
The fo= rmula is E =3D (1 / 4 pi E0) (q1 q2 / r12). =C2=A0 Thus your conversion fac= tor is 1 / (4 pi E0) where E0 =3D=C2=A08.854=C2=A0187=C2=A0817...=C2=A0x=C2= =A010-12=C2=A0 J^-1 C^2 m-1.
Sorry for the lack of typography.=C2=A0

=C2=A0 =C2=A0 On Thursday, May 12, 2016 10:33 AM, Richard Leo Wood rwoodphd= ##msn.com <owner-chemistry+/-ccl.net> wrote:



Sent to CCL by: "Richard Leo Wood" [rwoodphd ~~ msn.com]
I am trying to compute the electrostatic interaction for a pair of atoms > from an energy minimized structure.

I have the charges on the two atoms as -0.47 and -0.55.=C2=A0 They are 3.15=
Angstroms apart.=C2=A0 So, E =3D (-0.55*-0.45)e-38 C^2/3.15e-8 m.

I get 8.21e-32 C^2/m.=C2=A0 My question is how do I convert this to Joules?=

Richard



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<html><head></head><body><div style=3D"colo= r:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, H= elvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div = id=3D"yui_3_16_0_ym19_1_1463074875924_34604" dir=3D"ltr"= ;>The formula is E =3D (1 / 4 pi E0) (q1 q2 / r12). &nbsp; Thus your= conversion factor is 1 / (4 pi E0) where E0 =3D&nbsp;<b style=3D&qu= ot;color: rgb(255, 0, 0); font-family: monospace; font-size: large; white-s= pace: nowrap; background-color: rgb(204, 226, 243);" id=3D"yui_3_= 16_0_ym19_1_1463074875924_34936">8.854&nbsp;187&nbsp;817...= &nbsp;x&nbsp;10<sup id=3D"yui_3_16_0_ym19_1_1463074875924_3= 4937">-12</sup></b>&nbsp; J^-1 C^2 m-1.</div>= <div id=3D"yui_3_16_0_ym19_1_1463074875924_34604" dir=3D"= ltr"><br></div><div id=3D"yui_3_16_0_ym19_1_146= 3074875924_34604" dir=3D"ltr">Sorry for the lack of typog= raphy.&nbsp;</div> <div class=3D"qtdSeparateBR">&= lt;br><br></div><div class=3D"yahoo_quoted" sty= le=3D"display: block;"> <div style=3D"font-family: Hel= veticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; fo= nt-size: 13px;"> <div style=3D"font-family: HelveticaNeue, = Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16p= x;"> <div dir=3D"ltr"><font size=3D"2"= face=3D"Arial"> On Thursday, May 12, 2016 10:33 AM, Richard L= eo Wood rwoodphd##msn.com &lt;owner-chemistry+/-ccl.net&gt; wrote:<br></= font></div>=C2=A0 <br><br> <div class=3D"y_msg= _container"><br>Sent to CCL by: "Richard Leo Wood" = [rwoodphd ~~ msn.com]<br>I am trying to compute the electrostatic interactio= n for a pair of atoms <br>&gt; from an energy minimized structure= .<br><br>I have the charges on the two atoms as -0.47 and -0.55= .&nbsp; They are 3.15 <br>Angstroms apart.&nbsp; So, E =3D (-= 0.55*-0.45)e-38 C^2/3.15e-8 m.<br><br>I get 8.21e-32 C^2/m.&= ;nbsp; My question is how do I convert this to Joules?<br><br>R= ichard<br><br><br><br>-=3D This is automatically ad= ded to each message by the mailing script =3D-<br>To recover the emai= l address of the author of the message, please change<br>the strange = characters on the top line to the +/- sign. You can also<br>look up t= he X-Original-From: line in the mail header.<br><br>E-mail to s= ubscribers: <a ymailto=3D"mailto:CH= EMISTRY+/-ccl.net" href=3D"mailto:CH= EMISTRY+/-ccl.net">CHEMISTRY+/-ccl.net</a> or use:<br>&nbsp; = &nbsp; &nbsp; <a href=3D"http://www.c= cl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank"&g= t;http://www.ccl.net/cgi-bin/ccl/send_ccl_message= </a><br><br>E-mail to administrators: <a ymailto=3D&qu= ot;mailto:CHEMISTRY-REQUEST+/-<= a href=3D"http://ccl.net" rel=3D"noreferrer" target=3D"_blank">ccl.net&= quot; href=3D"mailto:CHEMISTRY= -REQUEST+/-ccl.net">CHEMISTRY-REQUEST+/-ccl.net</a> or use<br>&am= p;nbsp; &nbsp; &nbsp; <a href=3D"http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank= ">http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage</a><br><br<br>&nbsp; &nbsp; &nb= sp; <a href=3D"http://www.ccl.net/chemistry/sub_= unsub.shtml" target=3D"_blank">htt= p://www.ccl.net/chemistry/sub_unsub.shtml</a><br><br>= Before posting, check wait time at: <a href=3D"http://www.ccl.net/&qu= ot; target=3D"_blank">http://www.ccl.net</a><br><b= r>Job: <a href=3D"http://www.ccl.net/jobs" target=3D"= ;_blank">http://www.ccl.net/jobs </a><br>Conferences:= <a href=3D"http://server.ccl.net/= chemistry/announcements/conferences/" target=3D"_blank"&= gt;http://server.ccl.net/chemistry/announc= ements/conferences/</a><br><br>Search Messages: <a= href=3D"http://www.ccl.net/chemistry/searchc= cl/index.shtml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</a><b= r><br<br>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank"&g= t;http://www.ccl.net/spammers.txt</a><br><br>RT= FI: <a href=3D"http://www.ccl.net/chemist= ry/aboutccl/instructions/" target=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/&= lt;/a><br><br><br><br><br></div>=C2= =A0 </div> </div>=C2=A0 </div></div></body>&l= t;/html>

--94eb2c07c0b82b408c0532b59fe9-- From owner-chemistry@ccl.net Fri May 13 10:16:01 2016 From: "Gerard Pujadas gerard.pujadas-.-gmail.com" To: CCL Subject: CCL: DataBases Message-Id: <-52198-160513101505-28912-zHO1+AGUTyOSdtW4U5w2Xg#,#server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=001a11431a642ab5810532b9e607 Date: Fri, 13 May 2016 16:14:55 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas/./gmail.com] --001a11431a642ab5810532b9e607 Content-Type: text/plain; charset=UTF-8 Dear Sofia, the Tradicional Chinese Medicine database can be of interest for you. Please, download going here . Check also: http://chimiotheque-nationale.cn.cnrs.fr/ https://simtk.org/projects/sweetlead http://pkuxxj.pku.edu.cn/CVDHD/index.php http://pkuxxj.pku.edu.cn/UNPD/ http://foodb.ca/ https://sancdb.rubi.ru.ac.za/ Hope this helps Best Gerard 2016-05-10 17:00 GMT+02:00 Sofia Vasilakaki svasilak||chem.uoa.gr < owner-chemistry*_*ccl.net>: > > Sent to CCL by: "Sofia Vasilakaki" [svasilak]-[chem.uoa.gr] > Dear all, > > I would like to use a database of natural compounds from medicinal herbs > and plans in order to perform substructure search or virtual screening. I > have found some (super natural, gnps.ucsd.edu, nubbe.iq.unesp.br) but not > enough info about each compound and no mol2 files available for download. > I would appreciate it if you could share any links for similar databases. > > Also, could you suggest software tools like these in OpenEye and Maestro > packages, for performing calculations of structures properties (pKa, rule > of 5, ADME...)? > > Thank you! > > Kind Regards, > Sofia V.> > > -- Gerard Pujadas (PubMed publication list ) Cheminformatics & Nutrition Research Group http://orcid.org/0000-0003-2598-8089 Head of Biochemistry and Biotechnology Department phone +34 977 55 (9565) // skype account: gerard_pujadas Office 106, Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia --001a11431a642ab5810532b9e607 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Gerard

2016-05-10 17:00 GMT+02:00 Sofia Vasilakaki svasilak||chem.uoa.gr <owner-chemistry*_*ccl.net<= /a>>:

Sent to CCL by: "Sofia Vasilakaki" [svasilak]-[chem.uoa.gr]
Dear all,

I would like to use a database of natural compounds from medicinal herbs and plans in order to perform substructure search or virtual screening. I have found some (super natural, gnps.ucsd.edu, nubbe.iq.unesp.br) but not=
enough info about each compound and no mol2 files available for download. I would appreciate it if you could share any links for similar databases.
Also, could you suggest software tools like these in OpenEye and Maestro packages, for performing calculations of structures properties (pKa, rule of 5, ADME...)?

Thank you!

Kind Regards,
Sofia V.



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