From owner-chemistry@ccl.net Mon Nov 17 04:51:01 2014 From: "Sobia Ahsan Halim sobia_halim.:.yahoo.com" To: CCL Subject: CCL: Autodock docking dlg files into mol2 format Message-Id: <-50753-141117043344-23559-W2OYbZhCPGGDsppjaLWivg() server.ccl.net> X-Original-From: "Sobia Ahsan Halim" Date: Mon, 17 Nov 2014 04:33:42 -0500 Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim[a]yahoo.com] Dear All I have done virtual screening from AutoDock tools 4. Now I need to re-score the autodock results. Please let me know is there any script available for the extraction of top ranked docked conformation from dlg file and convert it into mol2 format. Thanks in advance Sobia From owner-chemistry@ccl.net Mon Nov 17 07:19:01 2014 From: "John McKelvey jmmckel _ gmail.com" To: CCL Subject: CCL: MS 7 and Loop Back Message-Id: <-50754-141117071820-8331-VO6HFctWMWUmiQg+fOhkLg*_*server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=047d7b676c4eced6e905080cf8ec Date: Mon, 17 Nov 2014 07:18:10 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel|,|gmail.com] --047d7b676c4eced6e905080cf8ec Content-Type: text/plain; charset=UTF-8 This is sort of off topic, but has consequences in ORCA. Does one have to have a physical loopback device for MS-7 or can it be done by the OS without the physical adaptor? If the latter how is it best done? Many thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel===gmail.com --047d7b676c4eced6e905080cf8ec Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
This is sort of off topic, but has consequences in OR= CA.=C2=A0 Does one have to have a physical loopback device for MS-7 or can = it be done by the OS without the physical adaptor?=C2=A0 If the latter how = is it best done?

Many thanks!

Joh= n

--
John= McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
<= a href=3D"mailto:jmmckel===gmail.com">jmmckel===gmail.com
--047d7b676c4eced6e905080cf8ec-- From owner-chemistry@ccl.net Mon Nov 17 09:31:01 2014 From: "Brian Skinn bskinn_-_alum.mit.edu" To: CCL Subject: CCL: MS 7 and Loop Back Message-Id: <-50755-141117093021-30847-5i7iRKXdCUe1ZRZnqoYEUQ[-]server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=047d7b3a833c3c601805080ed1ca Date: Mon, 17 Nov 2014 09:29:56 -0500 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn||alum.mit.edu] --047d7b3a833c3c601805080ed1ca Content-Type: text/plain; charset=UTF-8 John, A physical loopback adapter is not needed; to eliminate the loopback interface complaint from OpenMPI, see the following: https://cec.mpg.de/wikiorca/index.php/Windows_7_Installation_/_Execution I have experienced intermittent, silent hangs at the end of SCF/gradient cycles when running ORCA 3.0.2 in parallel on Win7 (never in serial). Per bugchucker's recommendation ( http://cec.mpg.de/forum/viewtopic.php?f=11&t=1314), I am testing with the addition of the OpenMPI btl_tcp_if_include=localhost (see the linked forum post for exactly what I've set up) but haven't run enough calculations yet to have an idea if it's working. Good luck, Brian On Mon, Nov 17, 2014 at 7:18 AM, John McKelvey jmmckel _ gmail.com < owner-chemistry%a%ccl.net> wrote: > This is sort of off topic, but has consequences in ORCA. Does one have to > have a physical loopback device for MS-7 or can it be done by the OS > without the physical adaptor? If the latter how is it best done? > > Many thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel]^[gmail.com > --047d7b3a833c3c601805080ed1ca Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
John,
A physic= al loopback adapter is not needed; to eliminate the loopback interface comp= laint from OpenMPI, see the following:=C2=A0htt= ps://cec.mpg.de/wikiorca/index.php/Windows_7_Installation_/_Execution

I have experienced= intermittent, silent hangs at the end of SCF/gradient cycles when running = ORCA 3.0.2 in parallel on Win7 (never in serial).=C2=A0 Per bugchucker'= s recommendation (http://cec.mpg.de/forum/viewtopic.php?f=3D11= &t=3D1314), I am testing with the addition of the OpenMPI btl_tcp_i= f_include=3Dlocalhost (see the linked forum post for exactly what I've = set up) but haven't run enough calculations yet to have an idea if it&#= 39;s working.

Good luck= ,
Brian

On Mon, N= ov 17, 2014 at 7:18 AM, John McKelvey jmmckel _ gmail.com <owner-chemistry%a%ccl.net> wrote:
This is sort of off topi= c, but has consequences in ORCA.=C2=A0 Does one have to have a physical loo= pback device for MS-7 or can it be done by the OS without the physical adap= tor?=C2=A0 If the latter how is it best done?

Many thanks= !

John

--
John McKelvey
10819 Middleford Pl
Ft = Wayne, IN 46818
260-489-2160
jmmckel]^[gmail.com

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