From owner-chemistry@ccl.net Sun Jul 25 15:28:01 2010 From: "lamees hegazy lameesshams%yahoo.com" To: CCL Subject: CCL:G: gaussian view and antechamber Message-Id: <-42346-100725152541-14980-2UvDrg0i7aOu/RjGoAbwNw-$-server.ccl.net> X-Original-From: lamees hegazy Content-Type: multipart/alternative; boundary="0-1352803351-1280085934=:33046" Date: Sun, 25 Jul 2010 12:25:34 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: lamees hegazy [lameesshams^^yahoo.com] --0-1352803351-1280085934=:33046 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Thank you Mahmoud for your suggessions. I'm simulating a ligand inside a pr= otein and I use gaussian view to edit some bond lengths and types but gauss= ian view changes completely the ligand coordinates. Is there any option in = gaussian view which lock the ligand in its original crustal structure coord= inates. 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 Subject: CCL:G: gaussian view and antechamber To: "HEGAZY, LAMEES " Date: Friday, July 23, 2010, 2:33 PM Dear AllI am really so sorry, I flipped it around."Dear LameesI don't remem= ber well what's the problem with mol2 file generated by GaussView.You can s= ave your file in Mol2 format by Gaussview, and then use OpenBabel to conver= t it to PDB. This PDB file works well with antechamber.=0AI have just one m= ore 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 P= BD format.=0A On Thu, Jul 22, 2010 at 1:28 PM, Mahmoud A. A. Ibrahim m.ibrahim]=3D[compch= em.net wrote: =0ADear LameesI don't remember well what's the problem with mol2 file gener= ated by GaussView.You can save your file in PDB formate by Gaussview, and t= hen use OpenBabel to convert it to mol2. This mol2 file works well with ant= echamber.=0A=0AI have just one more note, I do recommend to use R.E.D. soft= ware to generate your molecular charge, instead of antechamber.Sincerely;M.= Ibrahim On Thu, Jul 22, 2010 at 1:29 AM, lamees hegazy lameesshams=3Dyahoo.com wrote: =0A=0AHi 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.=20 =0A=0AAlso, I'm trying to use mol2 file generated by gaussian view in antec= hamber program but antechamber can't read the mol2 file. Does any one has t= hese errors before. =A0 =0A=0A =0A=0A=0A=0A=0A=0A=0A=0A =20 --=20 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0= =20 =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 University of Manchester, =0A=0A =A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,=20 =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 =A0Chemistry Department, =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty of Science, =0A =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University, =0A =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.=20 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information =A0 =A0 =A0 =A0 =A0 Email: m.ibrahim,+,compchem.net =0A=0A =A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +20862342601 =0A=0A --=20 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =A0 =A0=A0= =20 =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 University of Manchester, =0A=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL,=20 =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 Faculty of Science, =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia University, =0A=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.=20 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Contact Information =A0 =A0 =A0 =A0 =A0=A0 Email: m.ibrahim * compchem.net =0A=A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: www.compchem.net =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fax No.: +20862342601 =0A=0A=0A=0A=0A --0-1352803351-1280085934=:33046 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Thank you Mahmoud for your suggessions. I'm s= imulating a ligand inside a protein and I use gaussian view to edit some bo= nd lengths and types but gaussian view changes completely the ligand coordi= nates. Is there any option in gaussian view which lock the ligand in its or= iginal crustal structure coordinates.

Sincerely,
Lamees

--= - On Fri, 7/23/10, Mahmoud A. A. Ibrahim m.ibrahim#,#compchem.net <= ;owner-chemistry#,#ccl.net> wrote:
From: Mahmoud A. A. Ibrahim m.ibrahim#,#compchem.net <owner-chemistry#,#c= cl.net>
Subject: CCL:G: gaussian view and antechamber
To: "HEGAZY,= LAMEES " <lameesshams#,#yahoo.com>
Date: Friday, July 23, 2= 010, 2:33 PM

Dear All
I am really so so= rry, 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 con= vert it to PDB. This PDB file works well with antechamber.=0A
I have just one more note, I do recommend to use R.E.D. software= to generate your molecular charge, instead of antechamber.
Since= rely;
M. Ibrahim
"
RED software works on PBD= format.
=0A

On= Thu, Jul 22, 2010 at 1:28 PM, Mahmoud A. A. Ibrahim m.ibrahim]=3D[compchem.net <owner-chemistry * ccl.net> wrote:
=0ADear Lamees<= div>I don't remember well what's the problem with mol2 file generated by Ga= ussView.
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 an= techamber.
=0A=0A
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 lameess= hams=3Dyaho= o.com <owner-chemistry,+,ccl.net> wrote:
=0A=0A<= blockquote class=3D"yiv646373247gmail_quote" style=3D"border-left: 1px soli= d rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi CCl,<= br>
I'm trying to build a charged molecule using gaussian view and I don= 't find any option which allows me to do that.
=0A=0AAlso, I'm trying t= o use mol2 file generated by gaussian view in antechamber program but antec= hamber can't read the mol2 file. Does any one has these errors before.
<= br> 



=0A=0A
=0A=0A=0A=0A= =0A=0A=0A=0A


--
&nbs= p;                Mahmoud A. A. Ibr= ahim        
          &n= bsp;           Current Address
    &= nbsp;           7.05, School of Chemistry,
&nb= sp;            The University of Manchester,<= br>=0A=0A         Oxford Road, Manchester, M13 9PL,                     &nb= sp; United Kingdom.

             = ;          Home Address
      &= nbsp;          Chemistry Department,
  &n= bsp;                 Faculty of Sci= ence,
=0A                  =      Minia University,
=0A         &= nbsp;                 Minia 61519,<= br>                     &= nbsp;          Egypt.

     = ;               Contact Information
=           Email: m.ibrahim,+,compchem.net
=0A=0A   &nbs= p;          Website: www.compchem.net
  &= nbsp;               Fax No.: +2086234260= 1
=0A=0A


--
 =                 Mahmoud A. A. Ibra= him        
         =              Current Address
  =                7.05, School of Chem= istry,
              The University o= f Manchester,
=0A         Oxford Road, Manchest= er, M13 9PL,
                &n= bsp;      United Kingdom.

       =                 Home Address
&n= bsp;                 Chemistry Depa= rtment,
                  &= nbsp;  Faculty of Science,
           = ;             Minia University,
=0A  =                      = ;    Minia 61519,
            &n= bsp;                   Egypt. =

                  &nbs= p;  Contact Information
           Em= ail: m.ibrahi= m * compchem.net
=0A             = Website: www.compchem.net
            &nb= sp;      Fax No.: +20862342601
=0A=0A
=0A=0A --0-1352803351-1280085934=:33046-- From owner-chemistry@ccl.net Sun Jul 25 16:52:00 2010 From: "Matthew Clark mclark**pharmatrope.com" To: CCL Subject: CCL: autodock parameters Message-Id: <-42347-100725163331-8789-SvwO3v9EYYlNm2dkATHRnw^server.ccl.net> X-Original-From: Matthew Clark Content-Type: multipart/alternative; boundary="=-Z8/Z4Aq8DtgdHyYu7BGo" Date: Sun, 25 Jul 2010 16:33:24 -0400 Mime-Version: 1.0 Sent to CCL by: Matthew Clark [mclark|-|pharmatrope.com] --=-Z8/Z4Aq8DtgdHyYu7BGo Content-Type: text/plain Content-Transfer-Encoding: 7bit All, Is there an accepted set of settings for screening large databases of compounds for autodock? e.g. ga_run, ga_num_evals, ga_pop_size? I'm looking to screen about 1M compounds, and need a recommendation for settings that are fast, yet considered 'adequate'. I do have access to about 100 cpu's for this project, just to let you know of the computing capacity to go with the setting recommendations. Matt ________________________________________________________________________ Matthew Clark, Ph. D. CIO Pharmatrope Ltd 610 772 4652 mclark_-_pharmatrope.com --=-Z8/Z4Aq8DtgdHyYu7BGo Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 7bit
All,

Is there an accepted set of settings for screening large databases of compounds for autodock?
e.g. ga_run, ga_num_evals, ga_pop_size? 

I'm looking to screen about 1M compounds, and need a recommendation for settings that are fast, yet considered 'adequate'.   I do have access to about 100 cpu's for this project, just to let you know of the computing capacity to go with the setting recommendations.

Matt








Matthew Clark, Ph. D.
CIO Pharmatrope Ltd
610 772 4652
mclark_-_pharmatrope.com
--=-Z8/Z4Aq8DtgdHyYu7BGo-- From owner-chemistry@ccl.net Sun Jul 25 19:09:01 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600|*|gmail.com" To: CCL Subject: CCL:G: "Guess=Alter" not executed Message-Id: <-42348-100725190821-19716-brFwDM2sEJoBrV+3VzjTiA[A]server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=0016363b8f64c2317e048c3e5704 Date: Sun, 25 Jul 2010 18:08:14 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600[]gmail.com] --0016363b8f64c2317e048c3e5704 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I have a confusion about the "*Guess=Alter*" command in Gaussian03. I used this command to promote one unpaired electron from sigma orbital to pi orbital, in order to change the molecule form sigma radical to pi radical. However, the energy, charge and spin density are totally the same as before. Seems like it is not executed at all. I am pretty sure that I switched the correct orbitals and I kept the molecule under Cs symmetry all the time. Does anyone know what caused this failure? Thank you very much! Jane --0016363b8f64c2317e048c3e5704 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi All,
=A0
I have a confusion about the "Guess=3DAlter"= ; command in Gaussian03. I used this command to promote=A0one unpaired elec= tron from sigma orbital to pi orbital, in order to change the molecule form= sigma radical to pi radical. However, the energy, charge and spin density = are totally the same as before. Seems like it is not executed at all.
=A0
I am pretty sure that I switched the correct orbitals and I kept the m= olecule under Cs=A0symmetry all the time. Does anyone know=A0what caused th= is failure?=A0
=A0
Thank you very much!
=A0
Jane
--0016363b8f64c2317e048c3e5704-- From owner-chemistry@ccl.net Sun Jul 25 21:01:00 2010 From: "=?gb2312?B?0LvQobni?= xgxie{:}ynu.edu.cn" To: CCL Subject: CCL: "Guess=Alter" not executed Message-Id: <-42349-100725204928-507-3fzysTmoW2O0YesKpHzDpQ:-:server.ccl.net> X-Original-From: "=?gb2312?B?0LvQobni?=" Content-Type: multipart/alternative; boundary="----=_1280105360_8982.html" Date: Mon, 26 Jul 2010 08:49:20 +0800 Sent to CCL by: "=?gb2312?B?0LvQobni?=" [xgxie]_[ynu.edu.cn] ------=_1280105360_8982.html Content-Type: text/plain Content-Transfer-Encoding: base64 RGVhciBKYW5lLA0KS2V5d29yZCAiU0NGPVFDIiBtYXkgYmUgdXNlZnVsIGZvciBwcm9ibGVt LiB0aGFua3MuDQpHb29kIGx1Y2shDQpYaWFvZ3VhbmcgWGllDQpZdW5uYW4gdW5pdmVyc2l0 eQ0KDQrU2sT6tcTAtNDF1tDU+L6tzOG1vToNCj5Gcm9tOiAi0vO9oSBqYW5leWluNjAwfCp8 Z21haWwuY29tIiA8b3duZXItY2hlbWlzdHJ5QGNjbC5uZXQ+DQo+UmVwbHktVG86ICJDQ0wg U3Vic2NyaWJlcnMiIDxjaGVtaXN0cnlAY2NsLm5ldD4NCj5UbzogIlhpZSwgWGlhby1HdWFu ZyAtaWQjM2plLSIgPHhneGllQHludS5lZHUuY24+DQo+U3ViamVjdDogQ0NMOkc6IFwiR3Vl c3M9QWx0ZXJcIiBub3QgZXhlY3V0ZWQNCj5EYXRlOlN1biwgMjUgSnVsIDIwMTAgMTg6MDg6 MTQgLTA1MDANCj4NCj5IaSBBbGwsDQo+DQo+SSBoYXZlIGEgY29uZnVzaW9uIGFib3V0IHRo ZSAiKkd1ZXNzPUFsdGVyKiIgY29tbWFuZCBpbiBHYXVzc2lhbjAzLiBJIHVzZWQNCj50aGlz IGNvbW1hbmQgdG8gcHJvbW90ZSBvbmUgdW5wYWlyZWQgZWxlY3Ryb24gZnJvbSBzaWdtYSBv cmJpdGFsIHRvIHBpDQo+b3JiaXRhbCwgaW4gb3JkZXIgdG8gY2hhbmdlIHRoZSBtb2xlY3Vs ZSBmb3JtIHNpZ21hIHJhZGljYWwgdG8gcGkgcmFkaWNhbC4NCj5Ib3dldmVyLCB0aGUgZW5l cmd5LCBjaGFyZ2UgYW5kIHNwaW4gZGVuc2l0eSBhcmUgdG90YWxseSB0aGUgc2FtZSBhcyBi ZWZvcmUuDQo+U2VlbXMgbGlrZSBpdCBpcyBub3QgZXhlY3V0ZWQgYXQgYWxsLg0KPg0KPkkg YW0gcHJldHR5IHN1cmUgdGhhdCBJIHN3aXRjaGVkIHRoZSBjb3JyZWN0IG9yYml0YWxzIGFu ZCBJIGtlcHQgdGhlDQo+bW9sZWN1bGUgdW5kZXIgQ3Mgc3ltbWV0cnkgYWxsIHRoZSB0aW1l LiBEb2VzIGFueW9uZSBrbm93IHdoYXQgY2F1c2VkIHRoaXMNCj5mYWlsdXJlPw0KPg0KPlRo YW5rIHlvdSB2ZXJ5IG11Y2ghDQo+DQo+SmFuZQ0KPg0KPiAK ------=_1280105360_8982.html Content-Type: text/html Content-Transfer-Encoding: base64 PHA+RGVhciBKYW5lLDwvcD4NCjxwPktleXdvcmQgIlNDRj1RQyIgbWF5IGJlIHVzZWZ1bCBm b3IgcHJvYmxlbS4gdGhhbmtzLjwvcD4NCjxwPkdvb2QgbHVjayE8L3A+DQo8cD5YaWFvZ3Vh bmcgWGllPC9wPg0KPHA+WXVubmFuIHVuaXZlcnNpdHk8YnIgLz48YnIgLz7U2sT6tcTAtNDF 1tDU+L6tzOG1vTo8YnIgLz4mZ3Q7RnJvbTombmJzcDsi0vO9oSZuYnNwO2phbmV5aW42MDB8 KnxnbWFpbC5jb20iJm5ic3A7Jmx0O293bmVyLWNoZW1pc3RyeUBjY2wubmV0Jmd0OzxiciAv PiZndDtSZXBseS1UbzombmJzcDsiQ0NMJm5ic3A7U3Vic2NyaWJlcnMiJm5ic3A7Jmx0O2No ZW1pc3RyeUBjY2wubmV0Jmd0OzxiciAvPiZndDtUbzombmJzcDsiWGllLCZuYnNwO1hpYW8t R3VhbmcmbmJzcDstaWQjM2plLSImbmJzcDsmbHQ7eGd4aWVAeW51LmVkdS5jbiZndDs8YnIg Lz4mZ3Q7U3ViamVjdDombmJzcDtDQ0w6RzombmJzcDtcIkd1ZXNzPUFsdGVyXCImbmJzcDtu b3QmbmJzcDtleGVjdXRlZDxiciAvPiZndDtEYXRlOlN1biwmbmJzcDsyNSZuYnNwO0p1bCZu YnNwOzIwMTAmbmJzcDsxODowODoxNCZuYnNwOy0wNTAwPGJyIC8+Jmd0OzxiciAvPiZndDtI aSZuYnNwO0FsbCw8YnIgLz4mZ3Q7PGJyIC8+Jmd0O0kmbmJzcDtoYXZlJm5ic3A7YSZuYnNw O2NvbmZ1c2lvbiZuYnNwO2Fib3V0Jm5ic3A7dGhlJm5ic3A7IipHdWVzcz1BbHRlcioiJm5i c3A7Y29tbWFuZCZuYnNwO2luJm5ic3A7R2F1c3NpYW4wMy4mbmJzcDtJJm5ic3A7dXNlZDxi ciAvPiZndDt0aGlzJm5ic3A7Y29tbWFuZCZuYnNwO3RvJm5ic3A7cHJvbW90ZSZuYnNwO29u ZSZuYnNwO3VucGFpcmVkJm5ic3A7ZWxlY3Ryb24mbmJzcDtmcm9tJm5ic3A7c2lnbWEmbmJz cDtvcmJpdGFsJm5ic3A7dG8mbmJzcDtwaTxiciAvPiZndDtvcmJpdGFsLCZuYnNwO2luJm5i c3A7b3JkZXImbmJzcDt0byZuYnNwO2NoYW5nZSZuYnNwO3RoZSZuYnNwO21vbGVjdWxlJm5i c3A7Zm9ybSZuYnNwO3NpZ21hJm5ic3A7cmFkaWNhbCZuYnNwO3RvJm5ic3A7cGkmbmJzcDty YWRpY2FsLjxiciAvPiZndDtIb3dldmVyLCZuYnNwO3RoZSZuYnNwO2VuZXJneSwmbmJzcDtj aGFyZ2UmbmJzcDthbmQmbmJzcDtzcGluJm5ic3A7ZGVuc2l0eSZuYnNwO2FyZSZuYnNwO3Rv dGFsbHkmbmJzcDt0aGUmbmJzcDtzYW1lJm5ic3A7YXMmbmJzcDtiZWZvcmUuPGJyIC8+Jmd0 O1NlZW1zJm5ic3A7bGlrZSZuYnNwO2l0Jm5ic3A7aXMmbmJzcDtub3QmbmJzcDtleGVjdXRl ZCZuYnNwO2F0Jm5ic3A7YWxsLjxiciAvPiZndDs8YnIgLz4mZ3Q7SSZuYnNwO2FtJm5ic3A7 cHJldHR5Jm5ic3A7c3VyZSZuYnNwO3RoYXQmbmJzcDtJJm5ic3A7c3dpdGNoZWQmbmJzcDt0 aGUmbmJzcDtjb3JyZWN0Jm5ic3A7b3JiaXRhbHMmbmJzcDthbmQmbmJzcDtJJm5ic3A7a2Vw dCZuYnNwO3RoZTxiciAvPiZndDttb2xlY3VsZSZuYnNwO3VuZGVyJm5ic3A7Q3MmbmJzcDtz eW1tZXRyeSZuYnNwO2FsbCZuYnNwO3RoZSZuYnNwO3RpbWUuJm5ic3A7RG9lcyZuYnNwO2Fu eW9uZSZuYnNwO2tub3cmbmJzcDt3aGF0Jm5ic3A7Y2F1c2VkJm5ic3A7dGhpczxiciAvPiZn dDtmYWlsdXJlPzxiciAvPiZndDs8YnIgLz4mZ3Q7VGhhbmsmbmJzcDt5b3UmbmJzcDt2ZXJ5 Jm5ic3A7bXVjaCE8YnIgLz4mZ3Q7PGJyIC8+Jmd0O0phbmU8YnIgLz4mZ3Q7PGJyIC8+Jmd0 OyZuYnNwOzwvcD4= ------=_1280105360_8982.html--