From owner-chemistry@ccl.net Tue Jul 27 09:50:00 2010 From: "Lochana C Menikarachchi lochanac#%#yahoo.com" To: CCL Subject: CCL:G: Mass-Weighted Hessian Message-Id: <-42355-100727094645-24458-ZVPwqScAmXlHoZYl9Mq1eg|server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Tue, 27 Jul 2010 09:46:43 -0400 Sent to CCL by: "Lochana C Menikarachchi" [lochanac%x%yahoo.com] Hi All, Does anybody know a program that converts gaussian or jaguar generated Cartesian Hessian to a mass-weighted Cartesian hessian? Anybody familiar with Q2MM methods? I tried to contact the authors of this method but couldn't reach them. Thanks. Lochana From owner-chemistry@ccl.net Tue Jul 27 10:33:00 2010 From: "Sten Nilsson Lill stenil|,|chalmers.se" To: CCL Subject: CCL:G: Mass-Weighted Hessian Message-Id: <-42356-100727101534-15555-ISmGu4jlZYbxv+m8EApnPg%a%server.ccl.net> X-Original-From: Sten Nilsson Lill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 27 Jul 2010 16:15:22 +0200 MIME-Version: 1.0 Sent to CCL by: Sten Nilsson Lill [stenil%x%chalmers.se] Lochana, contact Prof. Per-Ola Norrby at University of Gothenburg, Sweden. He's the developer of Q2MM. This is the link to his webpage with contact details: http://sftp.che.chalmers.se/~pon/ Hope this helps, Sten Ph.D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg SE-412 96 Gothenburg, Sweden e-mail: stenil%a%chem.gu.se Phone: +46-31 786 9103 Fax: +46-31-772 3840 ________________________________________ > From: owner-chemistry+stenil==chem.gu.se%a%ccl.net [owner-chemistry+stenil==chem.gu.se%a%ccl.net] On Behalf Of Lochana C Menikarachchi lochanac#%#yahoo.com [owner-chemistry%a%ccl.net] Sent: Tuesday, July 27, 2010 3:46 PM To: Nilsson Lill, Sten Subject: CCL:G: Mass-Weighted Hessian Sent to CCL by: "Lochana C Menikarachchi" [lochanac%x%yahoo.com] Hi All, Does anybody know a program that converts gaussian or jaguar generated Cartesian Hessian to a mass-weighted Cartesian hessian? Anybody familiar with Q2MM methods? I tried to contact the authors of this method but couldn't reach them. Thanks. Lochanahttp://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 Tue Jul 27 11:07:00 2010 From: "Toon Verstraelen Toon.Verstraelen_-_UGent.be" To: CCL Subject: CCL:G: Mass-Weighted Hessian Message-Id: <-42357-100727104242-11165-mcAaYAYvYpSnQu6EFFZcpQ:+:server.ccl.net> X-Original-From: Toon Verstraelen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 Jul 2010 16:42:30 +0200 MIME-Version: 1.0 Sent to CCL by: Toon Verstraelen [Toon.Verstraelen^UGent.be] Hi Lochana, You just need to divide each column and each row by the square root of the mass of the corresponding atom. This is trivial to do in any almost any programming language. In Python (with the numpy library), it goes like this: hessian_mw = (hessian*mass_diag_inv_sqrt).transpose()*mass_diag_inv_sqrt where 'hessian' is the non-weighted Hessian, 'hessian_mw' is the weighted Hessian and mass_diag_inv_sqrt is a vector with the inverse of the square root of the masses. Note that in this vector, each atom mass is repeated three times, one for x, y and z. Such a vector is constructed starting from a vector of masses: masses3 = numpy.array([masses, masses, masses]).transpose().ravel() mass_diag_inv_sqrt = masses3**(-0.5) We did this (and much more) in the implementation of TAMkin. You may be interested in the program. Visit the website if you want to know more: https://molmod.ugent.be/code/wiki/TAMkin cheers, Toon On 07/27/2010 03:46 PM, Lochana C Menikarachchi lochanac#%#yahoo.com wrote: > Sent to CCL by: "Lochana C Menikarachchi" [lochanac%x%yahoo.com] > Hi All, > > Does anybody know a program that converts gaussian or jaguar generated Cartesian Hessian to a mass-weighted Cartesian hessian? Anybody familiar with Q2MM methods? I tried to contact the authors of this method but couldn't reach them. > > Thanks. > > Lochana> > -- Dr. ir. Toon Verstraelen Center for Molecular Modeling Ghent University Technologiepark 903, B9052 Zwijnaarde Belgium Tel: +32 9 264 65 56 E-mail: Toon.Verstraelen * UGent.be http://molmod.UGent.be/ http://molmod.UGent.be/code/ From owner-chemistry@ccl.net Tue Jul 27 11:43:00 2010 From: "Mannan K malie_03]|[yahoo.co.in" To: CCL Subject: CCL: virtual screening of salts Message-Id: <-42358-100727113640-6389-2S2NfeZBnB4bywAoHJMPQQ ~~ server.ccl.net> X-Original-From: "Mannan K" Date: Tue, 27 Jul 2010 11:36:39 -0400 Sent to CCL by: "Mannan K" [malie_03_-_yahoo.co.in] I have a set of small molecules which are reported to be a stong binders against a particular target, but these compounds are HCl salts, When I did docking study using these compounds, Cl- fly out separatly, Keeping N+(positively charged) compound during docking study is one method of doing docking, but I am not sure about the merits and demertis of this stratergy, If so these compounds may not behave (during docking) as like in experimental conditions Thank you so much for your time, From owner-chemistry@ccl.net Tue Jul 27 14:48:00 2010 From: "lamees hegazy lameesshams_._yahoo.com" To: CCL Subject: CCL: Histidine protonation states Message-Id: <-42359-100727144700-31062-fjDmGjwIwIqwH0UKaeFDTg:-:server.ccl.net> X-Original-From: lamees hegazy Content-Type: multipart/alternative; boundary="0-79090578-1280256413=:74867" Date: Tue, 27 Jul 2010 11:46:53 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: lamees hegazy [lameesshams#,#yahoo.com] --0-79090578-1280256413=:74867 Content-Type: text/plain; charset=us-ascii Dear CCL, How should I determine the HIS and CYS protonation states in a protein model before I run MD simulations. --0-79090578-1280256413=:74867 Content-Type: text/html; charset=us-ascii
Dear CCL,

How should I determine the HIS and CYS protonation states in a protein model before I run MD simulations.

--0-79090578-1280256413=:74867-- From owner-chemistry@ccl.net Tue Jul 27 15:58:00 2010 From: "Elaine Meng meng%a%cgl.ucsf.edu" To: CCL Subject: CCL: Histidine protonation states Message-Id: <-42360-100727153330-4053-166LQ3ChOeTGxnf2esdA1A|*|server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 27 Jul 2010 15:33:27 -0400 Sent to CCL by: "Elaine Meng" [meng^_^cgl.ucsf.edu] These pKa prediction web servers may be of interest: H++ http://biophysics.cs.vt.edu/H++/ PROPKA http://propka.ki.ku.dk/ ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 27, 2010, at 11:46 AM, lamees hegazy lameesshams_._yahoo.com wrote: Dear CCL, How should I determine the HIS and CYS protonation states in a protein model before I run MD simulations. From owner-chemistry@ccl.net Tue Jul 27 16:32:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim]|[compchem.net" To: CCL Subject: CCL: Histidine protonation states Message-Id: <-42361-100727155754-8947-Fqk45eP5S3z5OIOyLjKgOw[]server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0022159754e61d6940048c63e96e Date: Tue, 27 Jul 2010 20:57:27 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim::compchem.net] --0022159754e61d6940048c63e96e Content-Type: text/plain; charset=ISO-8859-1 Dear Lamess There are some programs study the protonation state of the amino residues, in addition to the group rotation. you can use MOE to help to by protonate 3D option and modify it in your pdb according to * Cysteine: (CYS) CYS: protonated form CYM: deprotonated or bonded to metal atom. CYX: involved in disulphide bridge and other bonds. * Histidine: (HIS) HID: protonated at delta position HIE: protonated at epsilon position HIP: protonated at both positions CB | CG / \ CD2 ND1 | | NE1---CE1 In this step, you may use Swiss-PDB viewer and select all HIS or CYS residues and start to look in 5ang. diameter around each one, depending on the chemical sense, change the name of the HIS and CYS according to their state. Sincerely; M. Ibrahim On Tue, Jul 27, 2010 at 7:46 PM, lamees hegazy lameesshams_._yahoo.com < owner-chemistry ~~ ccl.net> wrote: > Dear CCL, > > How should I determine the HIS and CYS protonation states in a protein > model before I run MD simulations. > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim ~~ compchem.net Website: www.compchem.net Fax No.: +20862342601 --0022159754e61d6940048c63e96e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Lamess

There are some = programs study the protonation state of the amino residues, in addition to = the group rotation.=A0

you can = use MOE to help to by protonate 3D option and=A0modify=A0it in your pdb acc= ording to

=A0=A0=A0 = * Cysteine: (CYS)

=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 CYS: protonated form

=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 CYM: deprotonated or bonded to metal atom.

=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 CYX: involved in disulphide bridge and other bonds.

=A0

=A0=A0=A0 = * Histidine: (HIS)

=A0=A0=A0= =A0=A0=A0=A0=A0 =A0=A0=A0=A0= HID: protonated at delta position

=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 HIE: protonated at epsilon position

=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 HIP: protonated at both positions=

=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 =A0CB
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0|
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0CG
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0/=A0 =A0 \
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 CD2=A0 =A0 ND1
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0 |=A0 =A0=A0=A0|
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 NE1---CE1

=A0= In this step, you may use Swiss-PDB viewer and select all HIS or CYS residues and start to look in 5ang. diameter around each one, depend= ing on the chemical sense, change the name of the HIS and CYS according to = their state.

Sincerely;

M. Ibrahim




On Tue, Jul 27, 2010 at 7:46 PM, lamees hegazy lameesshams_._yahoo.com <owner-chemistry ~~ ccl.net> wrote:
Dear CCL,=

How should I determine the HIS and CYS protonation states in a prot= ein model before I run MD simulations.




--
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =A0 =A0=A0
=A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Current Address
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0=A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Th= e University of Manchester,
=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fa= culty of Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia = University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Contact Information
=A0 =A0 = =A0 =A0 =A0=A0 Email: m.ibrahim ~~ c= ompchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fax No.: +2086= 2342601
--0022159754e61d6940048c63e96e-- From owner-chemistry@ccl.net Tue Jul 27 17:08:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim^_^compchem.net" To: CCL Subject: CCL:G: gaussian view and antechamber Message-Id: <-42362-100727160328-12774-Mif6ZI/QvI0XIWDpybNvxw(-)server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0022159754e61026ef048c63fee5 Date: Tue, 27 Jul 2010 21:03:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim/./compchem.net] --0022159754e61026ef048c63fee5 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL I have responded to this enquiry on her/his private email, the problem was not related to the file format. It was related to ligand modification inside the active site. It is solved by building a lib file for the modified ligand. Sincerely; M. Ibrahim On Sun, Jul 25, 2010 at 8:25 PM, lamees hegazy lameesshams%yahoo.com < owner-chemistry|*|ccl.net> wrote: > Thank you Mahmoud for your suggessions. I'm simulating a ligand inside a > protein and I use gaussian view to edit some bond lengths and types but > gaussian view changes completely the ligand coordinates. Is there any option > in gaussian view which lock the ligand in its original crustal structure > coordinates. > > Sincerely, > Lamees > > --- On *Fri, 7/23/10, Mahmoud A. A. Ibrahim m.ibrahim#,#compchem.net > * wrote: > > > From: Mahmoud A. A. Ibrahim m.ibrahim#,#compchem.net ccl.net> > Subject: CCL:G: gaussian view and antechamber > To: "HEGAZY, LAMEES " > Date: Friday, July 23, 2010, 2:33 PM > > Dear All > I am really so sorry, I flipped it around. > "Dear Lamees > I don't remember well what's the problem with mol2 file generated by > GaussView. > You can save your file in *Mol2* format by Gaussview, and then use > OpenBabel to convert it to *PDB*. This *PDB* file works well with > antechamber. > I have just one more note, I do recommend to use R.E.D. software to > generate your molecular charge, instead of antechamber. > Sincerely; > M. Ibrahim > " > *RED software works on PBD format.* > > On Thu, Jul 22, 2010 at 1:28 PM, Mahmoud A. A. Ibrahim m.ibrahim]=[ > compchem.net > > wrote: > > Dear Lamees > I don't remember well what's the problem with mol2 file generated by > GaussView. > You can save your file in PDB formate by Gaussview, and then use OpenBabel > to convert it to mol2. This mol2 file works well with antechamber. > I have just one more note, I do recommend to use R.E.D. software to > generate your molecular charge, instead of antechamber. > Sincerely; > M. Ibrahim > > On Thu, Jul 22, 2010 at 1:29 AM, lamees hegazy lameesshams=yahoo.com < > owner-chemistry,+,ccl.net > > wrote: > > Hi CCl, > > I'm trying to build a charged molecule using gaussian view and I don't find > any option which allows me to do that. > Also, I'm trying to use mol2 file generated by gaussian view in antechamber > program but antechamber can't read the mol2 file. Does any one has these > errors before. > > > > > > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim,+,compchem.net > Website: www.compchem.net > Fax No.: +20862342601 > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim * compchem.net > Website: www.compchem.net > Fax No.: +20862342601 > > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim|*|compchem.net Website: www.compchem.net Fax No.: +20862342601 --0022159754e61026ef048c63fee5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL
I have responded to this enquiry on her/his private email, the= problem was not related to the file format. It was related to ligand modif= ication inside the active site. It is solved by=A0building=A0a lib file for= the modified ligand.
Sincerely;
M. Ibrahim

On Sun, Jul 25, 2010 at 8:25 PM, lamees hegazy lameesshams%yahoo.com <owner-chemistry|*|ccl.net> wrote:
Thank you= Mahmoud for your suggessions. I'm simulating a ligand inside a protein= and I use gaussian view to edit some bond lengths and types but gaussian v= iew changes completely the ligand coordinates. Is there any option in gauss= ian view which lock the ligand in its original crustal structure coordinate= s.

Sincerely,
Lamees

--- On Fri, 7/23/10, Mahmoud A. A. Ibrah= im m.ibrahim#,#compchem.n= et <owner-chemistry],[ccl.net> wrote:

From: Mahmoud A. A. Ibrahim m.ibrahim#,#compchem.net <owner-chemistry]= ,[ccl.net>
Subject: CCL:G: gaussian view and antechamber
To: "HEGAZY, LAMEES &= quot; <lameesshams],[yaho= o.com>
Date: Friday, July 23, 2010, 2:33 PM

Dear All<= div> I am really so sorry, I flipped it around.
"Dear Lamees
I don't remember we= ll what's the problem with mol2 file generated by GaussView.
= You can save your file in Mol2 format by Gaussview, and then use Ope= nBabel to convert it to PDB. This PDB file works well with an= techamber.
I have just one more note, I do recommend to use R.E.D. software to ge= nerate your molecular charge, instead of antechamber.
Sincerely;<= /div>
M. Ibrahim
"
RED software works on PBD = format.

On Thu, Jul 22, 2010 at 1:28 PM, Mahmoud A. A. Ibrahim m.ibra= him]=3D[= compchem.net <owner-chemi= stry * ccl.net> wrote:
Dear Lamees
I don't remember well wha= t's the problem with mol2 file generated by GaussView.
You ca= n save your file in PDB formate by Gaussview, and then use OpenBabel to con= vert it to mol2. This mol2 file works well with antechamber.
I have just one more note, I do recommend to use R.E.D. software to ge= nerate your molecular charge, instead of antechamber.
Sincerely;<= /div>
M. Ibrahim

On Thu, Jul 22, 2010 at 1:29 AM, la= mees hegazy lameesshams=3Dyahoo.com <own= er-chemistry,+,ccl.net> wrote:
Hi CCl,

I'm trying to build a charged molecule using gaussian vi= ew and I don't find any option which allows me to do that.
Also, I'm trying to use mol2 file generated by gaussian view in antecha= mber program but antechamber can't read the mol2 file. Does any one has= these errors before.

=A0







--
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Univ= ersity of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim,+,compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 Fax No.: +20862342601



--
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =A0 =A0=A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0=A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 The Un= iversity of Manchester,
=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fa= culty of Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Contact Information
=A0 =A0 = =A0 =A0 =A0=A0 Email: m.ibrahim * compchem.net<= br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: www.compchem.net
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--
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--0022159754e61026ef048c63fee5-- From owner-chemistry@ccl.net Tue Jul 27 18:33:00 2010 From: "Tapas Kar tapas.kar!A!usu.edu" To: CCL Subject: CCL:G: Computational cost for CCSD(T) Message-Id: <-42363-100727183120-32699-U8S5dE6NcecHXrJ3Sk0TsA===server.ccl.net> X-Original-From: "Tapas Kar" Date: Tue, 27 Jul 2010 18:31:16 -0400 Sent to CCL by: "Tapas Kar" [tapas.kar(~)usu.edu] Hello experts, Any idea on how many cpu hours may require for CCSD(T) calculation on molecules with 330 to 410 basis functions (about 500-600 primitive Gaussian) using 16/24/32 processors in G09. Any suggestion on memory, scratch disk space and processors may require for such calculations? Thanks Tapas From owner-chemistry@ccl.net Tue Jul 27 19:31:00 2010 From: "Jamin Krinsky jamink^^berkeley.edu" To: CCL Subject: CCL:G: Computational cost for CCSD(T) Message-Id: <-42364-100727191817-20057-T6LRId/j8ATa682wA+PshA++server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09f8518fad180b0048c66b6d4 Date: Tue, 27 Jul 2010 16:18:08 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink[#]berkeley.edu] --00c09f8518fad180b0048c66b6d4 Content-Type: text/plain; charset=ISO-8859-1 Hi Tapas, To give you an idea, on our system a 24-atom molecule with 250 basis functions (about 530 primitives), run on 6 AMD Istanbul cores with 23GB RAM (all this is shared, not network), took about 50 cpu hours (total) and generated a 60GB rwf file. Now consider that CCSD(T) has an ON^3 disk requirement... Maybe this helps somewhat. Jamin On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu < owner-chemistry,,ccl.net> wrote: > > Sent to CCL by: "Tapas Kar" [tapas.kar(~)usu.edu] > Hello experts, > Any idea on how many cpu hours may require for CCSD(T) calculation on > molecules with 330 to 410 basis functions (about 500-600 primitive Gaussian) > using 16/24/32 processors in G09. Any suggestion on memory, scratch disk > space and processors may require for such calculations? > > Thanks > Tapas> > > -- 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 --00c09f8518fad180b0048c66b6d4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Tapas,

To give you an idea, on our system a 24-atom molecule with= 250 basis functions (about 530 primitives), run on 6 AMD Istanbul cores wi= th 23GB RAM (all this is shared, not network), took about 50 cpu hours (tot= al) and generated a 60GB rwf file. Now consider that CCSD(T) has an ON^3 di= sk requirement...

Maybe this helps somewhat.

Jamin


On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu <owner-chemistry,,ccl.net> wrote:

Sent to CCL by: "Tapas =A0Kar" [tapas.kar(~)usu.edu]
Hello experts,
Any idea on how many cpu hours may require for CCSD(T) calculation on molec= ules with 330 to 410 basis functions (about 500-600 primitive Gaussian) usi= ng 16/24/32 processors in G09. Any suggestion on memory, scratch disk space= and processors may require for such calculations?

Thanks
Tapas



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--
Jamin L Krinsky, Ph.D.<= br>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

--00c09f8518fad180b0048c66b6d4-- From owner-chemistry@ccl.net Tue Jul 27 21:34:00 2010 From: "David Gallagher gallagher.da_+_gmail.com" To: CCL Subject: CCL: ParaSurf 10 released Message-Id: <-42365-100727213224-16262-rl53W/IfJH0c7jMcFnyjkg!A!server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_29623781==.ALT" Date: Tue, 27 Jul 2010 18:27:19 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da-*-gmail.com] --=====================_29623781==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable New Release: ParaSurf 10 and the new Cepos Pipeline Pilot=20 components have been released.=20 Enhancements=20 include local electron affinity for Hamiltonians=20 with d-orbitals as polarization functions, the=20 PM6 Hamiltonian (70 elements), second generation=20 surface-integral models (local hydrophobicity),=20 molecular fragments, and atom-centered descriptors. Applications: =95 Cytochrome P450 drug metabolism prediction (with CypScore) =95 Ligand docking - improved accuracy =95 3D QSAR & QSPR - novel electronic descriptors =95 Chemical & physical property prediction... About ParaSurf: Quantum chemistry-based ParaSurf (TM), from Cepos=20 InSilico Ltd., calculates local electronic=20 surface properties of molecules that can be used=20 to predict Cytochrome P450 metabolism, provide=20 more accurate ligand docking, and predict a wide=20 range of physical and chemical properties. For more information: please visit=20 http://cacheresearch.com/cepos.html or Email Cepos*CACheResearch.com CAChe Research distributes and supports Cepos=20 InSilico products throughout north and south=20 America. UK-based Cepos Insilico Ltd. develops=20 and supports computational chemistry and=20 biochemistry technology from various research=20 institutions including University of Erlangan, Germany. =20 --=====================_29623781==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable New Release:
ParaSurf 10 and the new Cepos Pipeline Pilot components have been released.=20 Enhancements include local electron affinity for Hamiltonians with d-orbitals as polarization functions, the PM6 Hamiltonian (70 elements), second generation surface-integral models (local hydrophobicity), molecular fragments, and atom-centered descriptors.

Applications:
          =95   Cytochrome P450 drug metabolism prediction (with CypScore)
          =95   Ligand docking - improved accuracy
          =95   3D QSAR & QSPR - novel electronic descriptors
          =95   Chemical & physical property prediction...

About ParaSurf:
Quantum chemistry-based ParaSurf (TM), from Cepos InSilico Ltd., calculates local electronic surface properties of molecules that can be used to predict Cytochrome P450 metabolism, provide more accurate ligand docking, and predict a wide range of physical and chemical properties.

For more information:
please visit http://cacheresearch.com/cepos.html
or Email Cepos*CACheResearch.com

CAChe Research distributes and supports Cepos InSilico products throughout north and south America.  UK-based Cepos Insilico Ltd. develops and supports computational chemistry and biochemistry technology > from various research institutions including University of Erlangan, Germany. --=====================_29623781==.ALT--