From owner-chemistry@ccl.net Fri Jan 16 00:10:00 2009 From: "servaas servaas.michielssens=student.kuleuven.be" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38437-090115175350-9976-kC3jADUAzy4UQ8MwUVg/HA*server.ccl.net> X-Original-From: servaas Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 15 Jan 2009 23:21:30 +0100 Mime-Version: 1.0 Sent to CCL by: servaas [servaas.michielssens/./student.kuleuven.be] The ones I know of: autodock: http://autodock.scripps.edu/ Gromacs also has a clustering tool (g_cluster): www.gromacs.org kind regards, Servaas On Thu, 2009-01-15 at 13:08 -0500, Mohamed Abdulhameed mabdu3 +/-email.uky.edu wrote: > Sent to CCL by: "Mohamed Abdulhameed" [mabdu3:+:email.uky.edu] > Hello everyone, > > I had docked some 80 ligands to my target protein and got 100 docked poses for each ligand. I would like to cluster the poses (based on RMSD). I think this will help me to quickly select the more distinct poses. > > It will be helpful if anyone can tell me how I can do the clustering of poses. Is there any free software to do this? It will also be helpful if anyone can point out some links/websites towards clustering of compounds. > > Thank you for your time. > > regards, > Mohamed Diwan > Graduate student > College of Pharmacy > University of Kentucky> > From owner-chemistry@ccl.net Fri Jan 16 00:46:00 2009 From: "Madi madi7sk .. gmail.com" To: CCL Subject: CCL:G: G03, problem with PCM : ALPHA scaling factor with UAKS not read correctly Message-Id: <-38438-090115124128-16965-/jnGhlt/9Yox/Zi1nxF3Mw . server.ccl.net> X-Original-From: Madi Content-Type: multipart/alternative; boundary="----=_Part_9158_9721962.1232037268394" Date: Thu, 15 Jan 2009 11:34:28 -0500 MIME-Version: 1.0 Sent to CCL by: Madi [madi7sk^^^gmail.com] ------=_Part_9158_9721962.1232037268394 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, I had the same problem. As far as I understand, you will have to leave few lines blank. Just hit enter for a few lines (3-4) after you give your non-standard input. Hopefully that should take care of it. Madi On Wed, Jan 14, 2009 at 6:35 PM, Francesca Mocci francimocci .. tiscali.it < owner-chemistry^-^ccl.net> wrote: > Hi all, > > I'm using g03 revision C02 to optimize the structure of a molecule > modeling the solvent through PCM > defining the molecular cavity through the UAKS model > and using an electrostatic scaling factor for the sphere radius of 1.4 > > This is the input: > > %chk=uaks_1.4_ch3cn_6311gdp.chk > # pbe1pbe/6-311g(d,p) opt SCRF=(PCM,Read,Solvent=acetonitrile) > # freq > > 14gen09 > > 0 1 > coordinates of the system > > TABS=298. > RADII=UAKS > ALPHA=1.4 > > > > But the program seems not to read correctly the ALPHA input, infact in the > output file > it writes: > > Using the following non-standard input for PCM: > TABS=298. > RADII=UAKS > ALPHA=1.4 > --- end of non-standard input. > > ------------------------------------------------------------------------------ > United Atom Topological Model (UAKS parameters set). > Nord Group Hybr Charge Alpha Radius Bonded to > 1 C sp2 0.00 1.20 1.680 O2 [s] O7 [d] C8 [s] > 2 O sp3 0.00 1.20 1.500 C1 [s] C3 [s] > 3 CH3 sp3 0.00 1.20 1.950 O2 [s] > 7 O sp2 0.00 1.20 1.500 C1 [d] > 8 CH3 sp3 0.00 1.20 1.950 C1 [s] > > ------------------------------------------------------------------------------ > > If the cavity is defined with the UA0 model the ALPHA value is read > correctly: > > Using the following non-standard input for PCM: > TABS=298. > ALPHA=1.4 > --- end of non-standard input. > > ------------------------------------------------------------------------------ > United Atom Topological Model (UA0 parameters set). > Nord Group Hybr Charge Alpha Radius Bonded to > 1 C * 0.00 1.40 1.925 O2 [s] O7 [d] C8 [s] > 2 O * 0.00 1.40 1.750 C1 [s] C3 [s] > 3 CH3 * 0.00 1.40 2.525 O2 [s] > 7 O * 0.00 1.40 1.750 C1 [d] > 8 CH3 * 0.00 1.40 2.525 C1 [s] > > ------------------------------------------------------------------------------ > > Is this a bug or am I missing something? > Any hint on how to solve this problem would be very welcome! > > Best Regards, > Francesca Mocci > > > > > > > -- Asha for Education: Shall we labor so a child won't? http://www.workanhour.com ------=_Part_9158_9721962.1232037268394 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi,
I had the same problem.
As far as I understand, you will have to leave few lines blank.
Just hit enter for a few lines (3-4) after you give your non-standard input.
Hopefully that should take care of it.

Madi

On Wed, Jan 14, 2009 at 6:35 PM, Francesca Mocci francimocci .. tiscali.it <owner-chemistry^-^ccl.net> wrote:
Hi all,

I'm using g03 revision C02 to  optimize the structure of a molecule modeling the solvent through PCM
defining the molecular cavity through the UAKS model
and using an electrostatic scaling factor for the sphere radius of 1.4

This is the input:
%chk=uaks_1.4_ch3cn_6311gdp.chk
# pbe1pbe/6-311g(d,p) opt  SCRF=(PCM,Read,Solvent=acetonitrile)
# freq

14gen09

0 1
coordinates of the system

TABS=298.
RADII=UAKS
ALPHA=1.4


But the program seems not to read correctly the ALPHA input, infact in the output file
it writes:

Using the following non-standard input for PCM:
 TABS=298.
 RADII=UAKS
 ALPHA=1.4
 --- end of non-standard input.
 ------------------------------------------------------------------------------
 United Atom Topological Model (UAKS parameters set).
  Nord Group  Hybr  Charge Alpha Radius          Bonded to
    1   C     sp2   0.00   1.20  1.680   O2   [s]  O7   [d]  C8   [s]
    2   O     sp3   0.00   1.20  1.500   C1   [s]  C3   [s]
    3   CH3   sp3   0.00   1.20  1.950   O2   [s]
    7   O     sp2   0.00   1.20  1.500   C1   [d]
    8   CH3   sp3   0.00   1.20  1.950   C1   [s]
 ------------------------------------------------------------------------------
If the cavity is defined with the UA0 model the ALPHA value is read correctly:

 Using the following non-standard input for PCM:
 TABS=298.
 ALPHA=1.4
 --- end of non-standard input.
 ------------------------------------------------------------------------------
 United Atom Topological Model (UA0  parameters set).
  Nord Group  Hybr  Charge Alpha Radius          Bonded to
    1   C     *     0.00   1.40  1.925   O2   [s]  O7   [d]  C8   [s]
    2   O     *     0.00   1.40  1.750   C1   [s]  C3   [s]
    3   CH3   *     0.00   1.40  2.525   O2   [s]
    7   O     *     0.00   1.40  1.750   C1   [d]
    8   CH3   *     0.00   1.40  2.525   C1   [s]
 ------------------------------------------------------------------------------
Is this a bug or am  I missing something?
Any hint on how to solve this problem would be very welcome!

Best Regards,
Francesca Mocci





  



--
Asha for Education: Shall we labor so a child won't?
http://www.workanhour.com
------=_Part_9158_9721962.1232037268394-- From owner-chemistry@ccl.net Fri Jan 16 03:28:01 2009 From: "Mikko Vainio mikko.vainio^^abo.fi" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38439-090116023841-25057-gTFjY/jBE/pKXL9RFB0YNA_-_server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Jan 2009 09:07:44 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio^^^abo.fi] Hi Mohamed, Contactos is a free Python script that you can use to cluster poses. It eats mol2. The script lives here: http://web.abo.fi/~mhuhtala/contactos.html Cheers, Mikko Vainio Quoting "Mohamed Abdulhameed mabdu3+/-email.uky.edu" : > > Sent to CCL by: "Mohamed Abdulhameed" [mabdu3:+:email.uky.edu] > Hello everyone, > > I had docked some 80 ligands to my target protein and got 100 docked > poses for each ligand. I would like to cluster the poses (based on > RMSD). I think this will help me to quickly select the more distinct > poses. > > It will be helpful if anyone can tell me how I can do the clustering > of poses. Is there any free software to do this? It will also be > helpful if anyone can point out some links/websites towards > clustering of compounds. > > Thank you for your time. > > regards, > Mohamed Diwan > Graduate student > College of Pharmacy > University of Kentucky> > > > From owner-chemistry@ccl.net Fri Jan 16 04:03:01 2009 From: "Vincent Leroux vincent.leroux]*[loria.fr" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38440-090116035722-10930-LHMEcshjAE91Fd4PhkU8DA,server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Jan 2009 09:56:57 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux ~ loria.fr] Hi Mohamed, You should not cluster ligand poses blindly according to RMSD values, this can lead to severe errors. See : http://bioinfo-pharma.u-strasbg.fr/template/jd/pdf/publications/paper94.pdf All you can say for two ligands is the lower the RMSD, the higher the ***probability*** that the binding modes are similar. If you want to cluster all docked conformations for all ligands at the same time, this approach is much better for automated conformational clustering : http://pubs.acs.org/doi/abs/10.1021/ci7001507 But you have 100 poses per ligand - this is obviously too much so you should first perform filtering for each ligand. The docking program will probably be helpful in safely making the number of poses decrease dramatically. You should at least set it up in order to 1/ discard the poses that are predicted (even by the extremely approximate scoring function) to have a positive free energy of binding, and 2/ for semi-flexible docking, stop the calculations if the same best docking poses are obtained repetitively (e.g. RMSD < 1A 5 times) - no need to repeat 100 times a docking calculation that will always converge to the same result... Next I am supposing your docking program ranked the remaining poses somewhat. So I suggest you to save the best ranked pose as mol2 and generate a multi-mol2 file with all ranked poses, and to use VIDA (www.eyesopen.com) to do the filtering manually. VIDA is a commercial software but the whole OpenEye catalog is available for free to academics (renewable 1-year licence). The procedure is simple : - there is a module suited to displaying docking results - launch it with the target protein, the first ranked pose as the reference ligand and the multi-mol2 as docking results - you have the receptor surface and docked ligands displayed nicely - select the second ranked ligand to be displayed superimposed with the first - if you get the same binding mode, discard the second ligand, else keep it - display the third ligand and compare the docking mode to those you retained (the first and maybe the second) - process all docking poses... This will take some time for 80 ligands but you can trust what you obtain this way. I never had more than 5 docking poses selected even with the most flexible/troublesome ligands. In most cases you retain the top pose as all the others are obviously less interesting (same binding mode, or with missing interactions and no new one). If you have time you should experiment with the Sybzki minimizer (if you got the OpenEye licence, you should use it...). If you have say 10000 docked ligands I am sure you will not go for the manual selection - using a minimizer will make most docking poses for each ligand converge nicely to the same point. Just be careful with the program parameters, as with docking programs one mistake and you get garbage or ridiculously long calculations. VL servaas servaas.michielssens=student.kuleuven.be a écrit : > Sent to CCL by: servaas [servaas.michielssens/./student.kuleuven.be] > The ones I know of: > > autodock: http://autodock.scripps.edu/ > Gromacs also has a clustering tool (g_cluster): www.gromacs.org > > > kind regards, > > Servaas > > > On Thu, 2009-01-15 at 13:08 -0500, Mohamed Abdulhameed mabdu3 > +/-email.uky.edu wrote: > >> Sent to CCL by: "Mohamed Abdulhameed" [mabdu3:+:email.uky.edu] >> Hello everyone, >> >> I had docked some 80 ligands to my target protein and got 100 docked poses for each ligand. I would like to cluster the poses (based on RMSD). I think this will help me to quickly select the more distinct poses. >> >> It will be helpful if anyone can tell me how I can do the clustering of poses. Is there any free software to do this? It will also be helpful if anyone can point out some links/websites towards clustering of compounds. >> >> Thank you for your time. >> >> regards, >> Mohamed Diwan >> Graduate student >> College of Pharmacy >> University of Kentucky> >> >> From owner-chemistry@ccl.net Fri Jan 16 05:37:02 2009 From: "Francesca Mocci francimocci**tiscali.it" To: CCL Subject: CCL:G: G03, problem with PCM : ALPHA scaling factor with UAKS not read correctly Message-Id: <-38441-090116032755-28930-AwYmHlWwywaDr900rWo5Hw(~)server.ccl.net> X-Original-From: Francesca Mocci Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Jan 2009 09:27:35 +0100 MIME-Version: 1.0 Sent to CCL by: Francesca Mocci [francimocci!A!tiscali.it] Hi all, > As far as I understand, you will have to leave few lines blank. > Just hit enter for a few lines (3-4) after you give your non-standard > input. > Hopefully that should take care of it. > > Madi In my case entering few lines AFTER the non standard input didn't work, but entering a line BETWEEN the lines > RADII=UAKS > > ALPHA=1.4 did!! Thank you Madi for your help! Best regards, Francesca Mocci > > On Wed, Jan 14, 2009 at 6:35 PM, Francesca Mocci francimocci .. > tiscali.it > wrote: > > Hi all, > > I'm using g03 revision C02 to optimize the structure of a > molecule modeling the solvent through PCM > defining the molecular cavity through the UAKS model > and using an electrostatic scaling factor for the sphere radius of 1.4 > > This is the input: >> %chk=uaks_1.4_ch3cn_6311gdp.chk >> # pbe1pbe/6-311g(d,p) opt SCRF=(PCM,Read,Solvent=acetonitrile) >> # freq >> >> 14gen09 >> >> 0 1 >> coordinates of the system >> >> TABS=298. >> RADII=UAKS >> ALPHA=1.4 > > > But the program seems not to read correctly the ALPHA input, > infact in the output file > it writes: > >> Using the following non-standard input for PCM: >> TABS=298. >> RADII=UAKS >> ALPHA=1.4 >> --- end of non-standard input. >> ------------------------------------------------------------------------------ >> United Atom Topological Model (UAKS parameters set). >> Nord Group Hybr Charge Alpha Radius Bonded to >> 1 C sp2 0.00 1.20 1.680 O2 [s] O7 [d] C8 [s] >> 2 O sp3 0.00 1.20 1.500 C1 [s] C3 [s] >> 3 CH3 sp3 0.00 1.20 1.950 O2 [s] >> 7 O sp2 0.00 1.20 1.500 C1 [d] >> 8 CH3 sp3 0.00 1.20 1.950 C1 [s] >> ------------------------------------------------------------------------------ > If the cavity is defined with the UA0 model the ALPHA value is > read correctly: > >> Using the following non-standard input for PCM: >> TABS=298. >> ALPHA=1.4 >> --- end of non-standard input. >> ------------------------------------------------------------------------------ >> United Atom Topological Model (UA0 parameters set). >> Nord Group Hybr Charge Alpha Radius Bonded to >> 1 C * 0.00 1.40 1.925 O2 [s] O7 [d] C8 [s] >> 2 O * 0.00 1.40 1.750 C1 [s] C3 [s] >> 3 CH3 * 0.00 1.40 2.525 O2 [s] >> 7 O * 0.00 1.40 1.750 C1 [d] >> 8 CH3 * 0.00 1.40 2.525 C1 [s] >> ------------------------------------------------------------------------------ > Is this a bug or am I missing something? > Any hint on how to solve this problem would be very welcome! > > Best Regards, > Francesca Mocci > > > > > > > > > > > -- > Asha for Education: Shall we labor so a child won't? > http://www.workanhour.com From owner-chemistry@ccl.net Fri Jan 16 05:47:01 2009 From: "Michel PETITJEAN michel.petitjean|*|cea.fr" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38442-090116035508-9378-VWKuqX6h0j14HwZeBT0pzw###server.ccl.net> X-Original-From: "Michel PETITJEAN" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 16 Jan 2009 09:23:44 +0100 MIME-Version: 1.0 Sent to CCL by: "Michel PETITJEAN" [michel.petitjean{=}cea.fr] We have recently built a clustering program which generates or reads the array of RMSD distances and computes the optimal number of classes together with the mean point in each class. We used it for computing the representative conformers of a serie of ligands for virtual screening purposes, but it could be used to cluster poses as well. The method is described in a paper accepted in J. Chem. Inf. Model. and we are waiting for its publication. As soon as it will appear on the journal website, we will render public the freeware and announce it on the CCL list. Michel Petitjean DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean]_[cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.class.html ---------------- Sent to CCL by: "Mohamed Abdulhameed" [mabdu3:+:email.uky.edu] Hello everyone, I had docked some 80 ligands to my target protein and got 100 docked = poses for each ligand. I would like to cluster the poses (based on = RMSD). I think this will help me to quickly select the more distinct = poses.=20 It will be helpful if anyone can tell me how I can do the clustering of = poses. Is there any free software to do this? It will also be helpful if = anyone can point out some links/websites towards clustering of = compounds.=20 Thank you for your time. regards, Mohamed Diwan=20 Graduate student College of Pharmacy University of Kentucky From owner-chemistry@ccl.net Fri Jan 16 06:29:01 2009 From: "Aggelos Avramopoulos aggavramop,yahoo.gr" To: CCL Subject: CCL: CISD calculation and GAMESS Message-Id: <-38443-090116054412-28083-N2QJP4rB7JaarXNxntqBug::server.ccl.net> X-Original-From: Aggelos Avramopoulos Content-Type: multipart/alternative; boundary="0-1482864214-1232099278=:86327" Date: Fri, 16 Jan 2009 09:47:58 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Aggelos Avramopoulos [aggavramop^yahoo.gr] --0-1482864214-1232099278=:86327 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable DEAR CCLs I would like to make a CISD calculation in a diradical system by using GAME= SS. Actually i want to compute the transition dipole moment vector me1e2, betwe= en two excited states. Is it possible someone to=C2=A0 advise me how to do this type calculation. Thank you very much for any response. Aggelos Avramopoulos =C2=A0=0A=0A=0A =0A___________________________________________________= ________ =0A=CE=A7=CF=81=CE=B7=CF=83=CE=B9=CE=BC=CE=BF=CF=80=CE=BF=CE=B9=CE= =B5=CE=AF=CF=84=CE=B5 Yahoo!; =0A=CE=92=CE=B1=CF=81=CE=B5=CE=B8=CE=AE=CE=BA= =CE=B1=CF=84=CE=B5 =CF=84=CE=B1 =CE=B5=CE=BD=CE=BF=CF=87=CE=BB=CE=B7=CF=84= =CE=B9=CE=BA=CE=AC =CE=BC=CE=B7=CE=BD=CF=8D=CE=BC=CE=B1=CF=84=CE=B1 (spam);= =CE=A4=CE=BF Yahoo! Mail =0A=CE=B4=CE=B9=CE=B1=CE=B8=CE=AD=CF=84=CE=B5=CE= =B9 =CF=84=CE=B7=CE=BD =CE=BA=CE=B1=CE=BB=CF=8D=CF=84=CE=B5=CF=81=CE=B7 =CE= =B4=CF=85=CE=BD=CE=B1=CF=84=CE=AE =CF=80=CF=81=CE=BF=CF=83=CF=84=CE=B1=CF= =83=CE=AF=CE=B1 =CE=BA=CE=B1=CF=84=CE=AC =CF=84=CF=89=CE=BD =CE=B5=CE=BD=CE= =BF=CF=87=CE=BB=CE=B7=CF=84=CE=B9=CE=BA=CF=8E=CE=BD =0A=CE=BC=CE=B7=CE=BD= =CF=85=CE=BC=CE=AC=CF=84=CF=89=CE=BD http://login.yahoo.com/config/mail?.in= tl=3Dgr =0A --0-1482864214-1232099278=:86327 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
DEAR CCLs
I would like to make a CISD calculation in a diradical system by using= GAMESS.
Actually i want to compute the transition dipole moment vector me1e2, = between two
excited states.
Is it possible someone to  advise me how to do this type calculat= ion.
Thank you very much for any response.
Aggelos Avramopoulos
 

=0A=0A=0A=0A
=0A=CE=A7=CF=81=CE=B7=CF=83=CE=B9=CE=BC=CE=BF=CF= =80=CE=BF=CE=B9=CE=B5=CE=AF=CF=84=CE=B5 Yahoo!
=0A=CE=92=CE=B1=CF=81=CE= =B5=CE=B8=CE=AE=CE=BA=CE=B1=CF=84=CE=B5 =CF=84=CE=B1 =CE=B5=CE=BD=CE=BF=CF= =87=CE=BB=CE=B7=CF=84=CE=B9=CE=BA=CE=AC =CE=BC=CE=B7=CE=BD=CF=8D =CE=BC=CE= =B1=CF=84=CE=B1 (spam); =CE=A4=CE=BF Yahoo! Mail =CE=B4=CE=B9=CE=B1=CE=B8= =CE=AD=CF=84=CE=B5=CE=B9 =CF=84=CE=B7=CE=BD =CE=BA=CE=B1=CE=BB=CF=8D=CF=84= =CE=B5=CF=81=CE=B7 =CE=B4=CF=85=CE=BD=CE=B1=CF=84=CE=AE =CF=80=CF=81=CE=BF= =CF=83=CF=84=CE=B1=CF=83=CE=AF=CE=B1 =CE=BA=CE=B1=CF=84=CE=AC =CF=84=CF=89= =CE=BD =CE=B5=CE=BD=CE=BF=CF=87=CE=BB=CE=B7=CF=84=CE=B9=CE=BA=CF=8E=CE=BD = =CE=BC=CE=B7=CE=BD=CF=85=CE=BC=CE=AC=CF=84=CF=89=CE=BD
=0Ahttp://login.yahoo.com/config= /mail?.intl=3Dgr --0-1482864214-1232099278=:86327-- From owner-chemistry@ccl.net Fri Jan 16 09:29:01 2009 From: "Bikadi Zsolt zsolt.bikadi]^[virtuadrug.com" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38444-090115173034-8351-54DO3jncuE1sLWiNpsv0mg]=[server.ccl.net> X-Original-From: "Bikadi Zsolt" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Jan 2009 21:33:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Bikadi Zsolt" [zsolt.bikadi{:}virtuadrug.com] Hi, Your docking software should support clustering based on rmsd. What software do you use? For example in Autodock, you can use this dpf file to recluster your results: Command: autodock3 -p recluster.dpf -l recluster.dlg Whre the content of recluster.dpf should be: types CANOSH rmstol 2.0 write_all cluster results.dlg analysis Or use the recluster.py command of Autodock Tools. Alternatively, if you want to use a gui, than you can setup rmstol on Dockingserver (www.dockingserver.com), when you start a docking calculation. Or you can simply calculate the rmsds in Excel based on its definition: SQRT(1/n*SUM((x2-x1)^2+(y2-y1)^2+(z2-z1)^2)), so calculate the differences for each atom, sum the squares, divide by the number of atoms and the root of the result is rmsd. Sincerely, Zsolt -----Original Message----- > From: owner-chemistry+zsolt.bikadi==virtuadrug.com]![ccl.net [mailto:owner-chemistry+zsolt.bikadi==virtuadrug.com]![ccl.net] On Behalf Of Mohamed Abdulhameed mabdu3+/-email.uky.edu Sent: Thursday, January 15, 2009 7:08 PM To: Bikadi, Zsolt Subject: CCL: clustering docked poses Sent to CCL by: "Mohamed Abdulhameed" [mabdu3:+:email.uky.edu] Hello everyone, I had docked some 80 ligands to my target protein and got 100 docked poses for each ligand. I would like to cluster the poses (based on RMSD). I think this will help me to quickly select the more distinct poses. It will be helpful if anyone can tell me how I can do the clustering of poses. Is there any free software to do this? It will also be helpful if anyone can point out some links/websites towards clustering of compounds. Thank you for your time. regards, Mohamed Diwan Graduate student College of Pharmacy University of Kentuckyhttp://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 Fri Jan 16 10:04:00 2009 From: "Christopher Baker bmcmutations:gmail.com" To: CCL Subject: CCL: BMC Bioinformatics Special Issue: CALL FOR PAPERS - Mutations Message-Id: <-38445-090115233641-15259-uF/iNo5GcWLCce+QB+dQNQ##server.ccl.net> X-Original-From: "Christopher Baker" Date: Thu, 15 Jan 2009 23:36:37 -0500 Sent to CCL by: "Christopher Baker" [bmcmutations:gmail.com] ================================================= BMC Bioinformatics Special Issue: CALL FOR PAPERS ================================================= A special issue of the Journal will showcase original papers that address themes relevant to the: Annotation, Interpretation and Management of Mutations http://www.ebi.ac.uk/Rebholz-srv/aimm.html Mutations play a key role in the understanding of genetic mechanisms and complex diseases. A number of bioinformatics initiatives gather and store mutational relevant information (OMIM, GAD, HapMap, 1000 Genomces project, COSMIC, UniProtKb, PDB), but the challenge for data integration initiatives is to facilitate the interpretion of phenotypic / impact changes induced by the mutations. Solutions are required in the domains of: (i) text mining - for the identification of phenotypic / impact annotations, (ii) data warehousing and machine learning to allow better integration of mutation relevant information into a bioinformatics infrastructure (e.g., ontologies, workflows, databases, machine learning techniques). Synergistic use of these technologies should facilitate inferences of knowledge from sequence to structure to function and to phenotypes. Authors may also focus on methods for the prediction of phenotypic effects induced by mutations, infrastructure to support clinical decision processes involving mutations as well as the management and aggregation of mutations with annotations from different digital or text resources. Suggested themes (but not limted to): - Mutation Databases and Metadata: Design, Content, Accuracy. - Extraction of mutations and annotations from literature - Methods and systems for predicting the impacts of Mutations - Mutation Data Integration, Phenotype Ontologies, Semantic Support and Reuse Published manuscripts will include a clear and motivating description of the specific challenge and biological context that they address and a lucid illustration of the proposed solution. Article-processing charges: ======================= Please note that the standard BMC Bioinformatics publication processing fees apply to submissions to this special issue. Please refer to http://www.biomedcentral.com/bmcbioinformatics/ifora/ for further information. Important Dates: =============== Submissions open: Dec 25th 2008 Submissions due*: February 14th 2009 Revised manuscript submitted: March 31st 2009 Submissions: ============ Pre-submission enquiries and variations to the deadlines above may be made in consultation with the Special Issue Editor bakerc.##.unb.ca * Author instructions can be obtained by sending an email to bmcmutations.##.gmail.com an automated reply will sent and complete submissions should also be sent to bmcmutations.##.gmail.com but with AIMM in the subject line. Special Issue Editors: ====================== Christopher J. O. Baker - University of New Brunswick, Canada Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, UK From owner-chemistry@ccl.net Fri Jan 16 10:39:00 2009 From: "pasha shakoori pasha/./umail.ucsb.edu" To: CCL Subject: CCL: Z-Matrix rearrangements and dummy atoms Message-Id: <-38446-090116001331-25719-iYojhSRCLxzS1BfyIEW5/Q||server.ccl.net> X-Original-From: "pasha shakoori" Date: Fri, 16 Jan 2009 00:13:26 -0500 Sent to CCL by: "pasha shakoori" [pasha---umail.ucsb.edu] Hello, I was wondering if there is any organized, systematic method to arrange a Z-matrix to avoid "odd" angles. I am trying to convert pdb files to Z-mat and need to find an efficient way to do so. Thanks! pasha||umail.ucsb.edu From owner-chemistry@ccl.net Fri Jan 16 11:13:00 2009 From: "PETITJEAN Michel michel.petitjean%x%cea.fr" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38447-090116102824-1689-tPxz/Rzf5XEdC2jGLI5gEw(0)server.ccl.net> X-Original-From: "PETITJEAN Michel" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 16 Jan 2009 16:23:35 +0100 MIME-Version: 1.0 Sent to CCL by: "PETITJEAN Michel" [michel.petitjean:cea.fr] Does Excel minimizes the RMSD for all rotations and translations ? If not, you need a software such as ARMS or CSR. Michel Petitjean DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean*|*cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Sent to CCL by: "Bikadi Zsolt" [zsolt.bikadi{:}virtuadrug.com] > Hi, > > Your docking software should support clustering based on rmsd. What = software do you use? > > ... > > Or you can simply calculate the rmsds in Excel based on its = definition: > SQRT(1/n*SUM((x2-x1)^2+(y2-y1)^2+(z2-z1)^2)), so calculate the = differences > for each atom, sum the squares, divide by the number of atoms and the = root > of the result is rmsd. > > Sincerely, > Zsolt From owner-chemistry@ccl.net Fri Jan 16 12:17:01 2009 From: "Geoffrey Hutchison geoffh+[a]pitt.edu" To: CCL Subject: CCL:G: Z-Matrix rearrangements and dummy atoms Message-Id: <-38448-090116120534-10142-IzfIU0SEw1VFQJZs89gltw-,-server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 7bit Content-type: text/plain; delsp=yes; format=flowed; charset=US-ASCII Date: Fri, 16 Jan 2009 12:05:21 -0500 MIME-version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Geoffrey Hutchison [geoffh+++pitt.edu] On Jan 16, 2009, at 12:13 AM, pasha shakoori pasha/./umail.ucsb.edu wrote: > I was wondering if there is any organized, systematic method to > arrange a Z-matrix to avoid "odd" angles. I am trying to convert pdb > files to Z-mat and need to find an efficient way to do so. If it's a large enough molecule, it's usually possible to find atoms which avoid "bad" angles and torsions. Usually the solution is somewhat brute-force -- rather than only using bonded atoms for the z- matrix, the code goes through non-bonded pairs. If you're converting PDB to z-matrix, you probably want to look at Open Babel, which does this automatically (e.g., convert to gzmat = Gaussian z-matrix). http://openbabel.org/ If you want to code this yourself, take a look at our code, which is open source. Look for CartesianToInternal. It's not "beautiful," but it's been heavily tested and refined over the years. http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/obutil.cpp?view=markup Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh_+_pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Fri Jan 16 13:02:01 2009 From: "Herbert Fruchtl herbert.fruchtl.:.st-andrews.ac.uk" To: CCL Subject: CCL: Z-Matrix rearrangements and dummy atoms Message-Id: <-38449-090116121419-12125-Va8hSlnRb3q68lcMh2n++Q|,|server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 16 Jan 2009 16:42:44 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl~!~st-andrews.ac.uk] I don't know of a systematic way. I had good experiences with Gaussview (if you have it; it's commercial): read in an input with Cartesian coordinates and write it as Z-Matrix. The choice of distances and angles is usually reasonable. Herbert pasha shakoori pasha/./umail.ucsb.edu wrote: > Sent to CCL by: "pasha shakoori" [pasha---umail.ucsb.edu] > Hello, > I was wondering if there is any organized, systematic method to arrange a Z-matrix to avoid "odd" angles. I am trying to convert pdb files to Z-mat and need to find an efficient way to do so. > Thanks! > > pasha*|*umail.ucsb.edu> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Jan 16 16:39:00 2009 From: "maxim totrov max[A]molsoft.com" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38450-090116150752-14656-y74AjLoSK1YhPTmF+gDonA.:.server.ccl.net> X-Original-From: maxim totrov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 16 Jan 2009 10:40:08 -0800 Mime-Version: 1.0 (Apple Message framework v929.2) Sent to CCL by: maxim totrov [max*o*molsoft.com] For docking poses (as opposed to conformational analysis), you usually do not want to minimize RMSD for rotations and translations (RMSD with superposition). As an extreme case, consider completely rigid ligand: you still might have many distinct docked poses, but RMSD with superposition will always be zero. On the other hand, an important issue arises if there are symmetric moieties in your molecules - one has to consider different possible correspondences between equivalent atoms in two poses. Think of a flipping phenyl moiety for example. Excel will not detect that. Among other software, Molsoft's free Browser can calculate either static or superimposed RMSDs, with or without consideration of symmetries. Scripting language allows easy batch processing. Best regards, Max Totrov > > Sent to CCL by: "PETITJEAN Michel" [michel.petitjean:cea.fr] > > Does Excel minimizes the RMSD for all rotations and translations ? > If not, you need a software such as ARMS or CSR. > > Michel Petitjean > DSV/iBiTec-S/SB2SM (CNRS URA 2096) > CEA Saclay, bat. 528 > 91191 Gif-sur-Yvette Cedex, France. > Phone: +331 6908 4006 / Fax: +331 6908 4007 > E-mail: michel.petitjean^^cea.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > > > Sent to CCL by: "Bikadi Zsolt" [zsolt.bikadi{:}virtuadrug.com] >> Hi, >> >> Your docking software should support clustering based on rmsd. What >> software do you use? >> >> ... >> >> Or you can simply calculate the rmsds in Excel based on its >> definition: >> SQRT(1/n*SUM((x2-x1)^2+(y2-y1)^2+(z2-z1)^2)), so calculate the >> differences >> for each atom, sum the squares, divide by the number of atoms and >> the root >> of the result is rmsd. >> >> Sincerely, >> Zsolt > > > > -To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Fri Jan 16 20:12:00 2009 From: "Kianoush Mirsanaei k.mirsanaie!=!yahoo.com" To: CCL Subject: CCL: Water Molecule Simulation Message-Id: <-38451-090116185723-1135-QUMMMr75MM7wzm02Pim1ig(-)server.ccl.net> X-Original-From: "Kianoush Mirsanaei" Date: Fri, 16 Jan 2009 18:57:19 -0500 Sent to CCL by: "Kianoush Mirsanaei" [k.mirsanaie()yahoo.com] Hello Everybody, I am asking if anybody can advise me with the fortran code of water molecules simulation(To calculate forces and potential). Best Regards Kianoush