From owner-chemistry@ccl.net Thu Oct 29 00:07:00 2009
From: "Wenli Zou zorkzou : gmail.com" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: a dangerous bug in generating .wfn file by RO-HF/RO-DFT
Message-Id: <-40548-091029000506-25983-gtvYJwapujSrFo5NB0D/7w ~ server.ccl.net>
X-Original-From: "Wenli  Zou" <zorkzou[a]gmail.com>
Date: Thu, 29 Oct 2009 00:05:02 -0400


Sent to CCL by: "Wenli  Zou" [zorkzou(a)gmail.com]
Hi all,

In the .wfn file generated by RO-HF/RO-DFT calculation, all the singly occupied orbitals have the occ. number=2.00 by error. So the subsequent analysis by AIMPAC/AIM2000/AIMALL... will be wrong.

The occupation numbers can be corrected by hand.

Wenli


From owner-chemistry@ccl.net Thu Oct 29 00:41:01 2009
From: "Wenli Zou zorkzou-$-gmail.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Gaussian03 error in generating .wfn file
Message-Id: <-40549-091029000825-27090-SKTXsQDzZrfzNayX9s7ARQ * server.ccl.net>
X-Original-From: "Wenli  Zou" <zorkzou-x-gmail.com>
Date: Thu, 29 Oct 2009 00:08:21 -0400


Sent to CCL by: "Wenli  Zou" [zorkzou-#-gmail.com]
Hi Adil,
 
The error "IPrim.ne.NPrim in ShlToP" is resulted from g-, h-, or higher basis functions. Please delete these basis functions from the basis set (c.f. GEN and GENECP) or use smaller basis set.
Alternatively, please try GAMESS if you prefer g-functions.
 
Wenli


From owner-chemistry@ccl.net Thu Oct 29 02:26:01 2009
From: "Gerard Pujadas gerard.pujadas]-[gmail.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?
Message-Id: <-40550-091028222300-22370-XunOmlIblBAHoklGfeC3+g.@.server.ccl.net>
X-Original-From: Gerard Pujadas <gerard.pujadas_._gmail.com>
Content-Type: multipart/alternative; boundary=0016e6db2d23c552760477088a59
Date: Thu, 29 Oct 2009 02:07:58 +0100
MIME-Version: 1.0


Sent to CCL by: Gerard Pujadas [gerard.pujadas]_[gmail.com]
--0016e6db2d23c552760477088a59
Content-Type: text/plain; charset=ISO-8859-1

Dear CCL subscribers,

is any one in the list running ROCS and VIDA (from OpenEye) with the 64bits
version of Ubuntu (I currently have version 9.04 installed on my computer)?

I have installed in my computer the eon-2.0.1-suse-9.1-x86_64.tar.gz file
and the resulting EON software runs perfectly. Nevertheless, when
I tried to run the ROCS or VIDA downloaded from the same page that EON
(rocs-2.4.2-suse-9.1-x64.tar.gz and vida-4.0.0-suse-9.1-x64.tar.gz files,
respectively), the next error messages appear:


esther]*[nutrigenomica002:~$ vida

ERROR: Unable to find an appropriate installation of vida for
       this architecture (linux-2.6-x64).

       Available compatible installations of vida:

which would be a "compatible installation" of vida? could you suggest which
are the .tar.gz files that we have to download from the OpenEye website in
order to use ROCS and VIDA?

I have asked this also to support]*[eyesopen.com but they have replyed me that
their software is not supported in Ubuntu ...

With many thanks in advances for your help and time

Yours sincerely

Gerard

--0016e6db2d23c552760477088a59
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<br><div class=3D"gmail_quote">Dear CCL subscribers,<br><br>is any one in t=
he list running ROCS and VIDA (from OpenEye) with the 64bits version of Ubu=
ntu (I currently have version 9.04 installed on my computer)?<br><br>I have=
 installed in my computer the eon-2.0.1-suse-9.1-x86_64.tar.gz file and the=
 resulting EON software runs perfectly. Nevertheless, when <div>

I tried to run the ROCS or VIDA downloaded from the same page that EON (roc=
s-2.4.2-suse-9.1-x64.tar.gz and vida-4.0.0-suse-9.1-x64.tar.gz files, respe=
ctively), the next error messages appear:<br><br>


<br>esther]*[nutrigenomica002:~$ vida<br><br>ERROR: Unable to find an appropr=
iate installation of vida for<br>=A0=A0=A0=A0=A0=A0 this architecture (linu=
x-2.6-x64).<br>=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 <br>=A0=A0=A0=A0=A0=A0 Available compatib=
le installations of vida:<br>




<br>which would be a &quot;compatible installation&quot; of vida? could you
suggest which are the .tar.gz files that we have to download from the OpenE=
ye website in order
to use ROCS and VIDA?<br><br> I have asked this also to <a href=3D"mailto:s=
upport]*[eyesopen.com" target=3D"_blank">support]*[eyesopen.com</a> but they ha=
ve replyed me that their software is not supported in Ubuntu ...<br><br>Wit=
h many thanks in advances for your help and time<br>


<br>Yours sincerely<br><font color=3D"#888888"><font color=3D"#888888"><br>=
Gerard</font></font></div>
</div><br>

--0016e6db2d23c552760477088a59--


From owner-chemistry@ccl.net Thu Oct 29 05:13:00 2009
From: "Hofmann, Alexander Alexander.Hofmann.:.eu.umicore.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: AW: G: Running gaussian on a cluster ...
Message-Id: <-40551-091029043557-30743-jD7o1Y8CvgcWISP6NXIMiw{=}server.ccl.net>
X-Original-From: "Hofmann, Alexander" <Alexander.Hofmann]-[eu.umicore.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: quoted-printable
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 charset=iso-8859-1
Date: Thu, 29 Oct 2009 09:03:35 +0100
MIME-Version: 1.0


Sent to CCL by: "Hofmann, Alexander" [Alexander.Hofmann||eu.umicore.com]
Hi,

I had a similar problem using a queuing system. Here the scripts =
starting the local demons on the nodes had a memory limit. Since =
'ulimit' did not do the job, I'm starting the demons by hand (from the =
shell) and the error disappeared.

Hth

Alex

> -----Urspr=FCngliche Nachricht-----
> Von: owner-chemistry+alexander.hofmann=3D=3Deu.umicore.com[#]ccl.net
> [mailto:owner-chemistry+alexander.hofmann=3D=3Deu.umicore.com[#]ccl.net] =
Im
> Auftrag von Denis Gulin deninho++quimica.ufpr.br
> Gesendet: Mittwoch, 28. Oktober 2009 15:21
> An: Hofmann, Alexander
> Betreff: CCL:G: Running gaussian on a cluster ...
>=20
>=20
> Sent to CCL by: "Denis Gulin" [deninho-.-quimica.ufpr.br]
>=20
> Hi CCLers,
>=20
> Recently we've upgrade Gaussian03 to Revision E.01. The compilation =
(with
> Portland compilers) has finished fine. Jobs also run fine in the main =
node
> of our cluster but, when we try run Gaussian on other node (processor
> servers), it fails. These other nodes doesn't have local hard disks =
so,
> the system is mounted from the main node, as NFS.
>=20
> When the jobs fail, we receive the error massage: "buffer allocation
> failed in ntrext1.: Cannot allocate memory" and a line "buffer =
allocation
> failed in ntrext1." is printed in the log file.
>=20
> My question is: There is something to do, for this 'limitation' for
> running Gaussian on networking file systems, like NFS ? How can I =
overcome
> this problem ? Any ideas ?
>=20
> Thanks in advance,
>=20
> Regards,
>=20
> -- Denis Jeison Gulin --
>  deninho|*|quimica.ufpr.br
> Laborat=F3rio de Qu=EDmica Computational
> Universidade Federal do Paran=E1 - UFPR
> Centro Polit=E9cnico
> P.O.Box 19081
> 81531-990 Curitiba/PR - Brazil
>=20
>=20
>=20
> -=3D This is automatically added to each message by the mailing script =
=3D-
> To recover the email address of the author of the message, please =
change>=20>=20>=20>=20>=20> Conferences: =
http://server.ccl.net/chemistry/announcements/conferences/
>=20>=20>=20>=20
>=20


From owner-chemistry@ccl.net Thu Oct 29 06:28:00 2009
From: "Daniel Jana dfjana{=}gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Running gaussian on a cluster ...
Message-Id: <-40552-091029062018-1199-VgvqL1QJO2061lfbZOk+Sg++server.ccl.net>
X-Original-From: Daniel Jana <dfjana_._gmail.com>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 29 Oct 2009 11:20:03 +0100
MIME-Version: 1.0


Sent to CCL by: Daniel Jana [dfjana|-|gmail.com]
Ol=E1,

We faced this same problem while using PBS as a queuing system (not
with SGE though).

The problem seems to be related (solely) to the check file. We solved
the situation by putting the chk in the node itself and the copying it
back to the main server in the end of the calculation. For us this was
easy since we have disks for scratch in every node. If you can't find
another solution, maybe creating a ramdisk big enough for the typical
chk file sizes you have may help solve the issue.

Boa sorte com isso,
Daniel

2009/10/28 Denis Gulin deninho++quimica.ufpr.br <owner-chemistry#ccl.net>:
>
> Sent to CCL by: "Denis Gulin" [deninho-.-quimica.ufpr.br]
>
> Hi CCLers,
>
> Recently we've upgrade Gaussian03 to Revision E.01. The compilation (with
> Portland compilers) has finished fine. Jobs also run fine in the main nod=
e
> of our cluster but, when we try run Gaussian on other node (processor
> servers), it fails. These other nodes doesn't have local hard disks so,
> the system is mounted from the main node, as NFS.
>
> When the jobs fail, we receive the error massage: "buffer allocation
> failed in ntrext1.: Cannot allocate memory" and a line "buffer allocation
> failed in ntrext1." is printed in the log file.
>
> My question is: There is something to do, for this 'limitation' for
> running Gaussian on networking file systems, like NFS ? How can I overcom=
e
> this problem ? Any ideas ?
>
> Thanks in advance,
>
> Regards,
>
> -- Denis Jeison Gulin --
> =A0deninho|*|quimica.ufpr.br
> Laborat=F3rio de Qu=EDmica Computational
> Universidade Federal do Paran=E1 - UFPR
> Centro Polit=E9cnico
> P.O.Box 19081
> 81531-990 Curitiba/PR - Brazil
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt>
>
>


From owner-chemistry@ccl.net Thu Oct 29 08:25:01 2009
From: "Basma Ghazal basmaghazal{:}ymail.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: explanation
Message-Id: <-40553-091029081821-19792-OdixjIiI30XsIYGC4FyTvg|a|server.ccl.net>
X-Original-From: Basma Ghazal <basmaghazal#,#ymail.com>
Content-Type: multipart/alternative; boundary="0-1123784454-1256815055=:56483"
Date: Thu, 29 Oct 2009 04:17:35 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Basma Ghazal [basmaghazal#,#ymail.com]
--0-1123784454-1256815055=:56483
Content-Type: text/plain; charset=us-ascii

Dear CClers:
I want to know why we delete hydrogen atoms from the pdb structure and then add the polar onewhen we prepare it for docking?
What is the different between the polar and non polar.
I will be appreciate if any one reply.
Thanks,


      
--0-1123784454-1256815055=:56483
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<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:tahoma, new york, times, serif;font-size:14pt"><P>Dear CClers:</P>
<P>I want to know why we delete hydrogen atoms from the pdb structure and then add the polar onewhen we prepare it for docking?</P>
<P>What is the different between the polar and non polar.</P>
<P>I will be appreciate if any one reply.</P>
<P>Thanks,</P></div><br>



      </body></html>
--0-1123784454-1256815055=:56483--


From owner-chemistry@ccl.net Thu Oct 29 10:15:01 2009
From: "Vincent Leroux vincent.leroux^^loria.fr" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?
Message-Id: <-40554-091029101245-24290-JtNA8j9XeB1A/V7pffb/hA*server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux!A!loria.fr>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 29 Oct 2009 15:12:32 +0100
MIME-Version: 1.0


Sent to CCL by: Vincent Leroux [vincent.leroux]|[loria.fr]
Hi Gerard,

First, pick up the SLED10-x64 versions.
They work well on my 8.04 64-bit Ubuntu system, this should also be the 
case on 9.04.

If you still have problems, I suggest editing the uselessly complicated 
(and definitely not Ubuntu-friendly) program launch script (it should be 
in openeye/bin/, the actual executable being located in 
arch/suse-SLED10-x64/program/version/bin/).

Delete / comment out the initializations

ostype="unknown"
osver=`uname -r ...`
arch=""

then replace by:

ostype=suse
osver=SLED10
arch=x64

then delete / comment out the whole case...esac construct just afterwards.
This will make sure that the script will not hopelessly try to determine 
the system architecture by itself.

This might do the trick.

Regards,
Vincent Leroux



Gerard Pujadas gerard.pujadas]-[gmail.com a écrit :
>
> Dear CCL subscribers,
>
> is any one in the list running ROCS and VIDA (from OpenEye) with the 
> 64bits version of Ubuntu (I currently have version 9.04 installed on 
> my computer)?
>
> I have installed in my computer the eon-2.0.1-suse-9.1-x86_64.tar.gz 
> file and the resulting EON software runs perfectly. Nevertheless, when
> I tried to run the ROCS or VIDA downloaded from the same page that EON 
> (rocs-2.4.2-suse-9.1-x64.tar.gz and vida-4.0.0-suse-9.1-x64.tar.gz 
> files, respectively), the next error messages appear:
>
>
> esther]*[nutrigenomica002:~$ vida
>
> ERROR: Unable to find an appropriate installation of vida for
>        this architecture (linux-2.6-x64).
>                                
>        Available compatible installations of vida:
>
> which would be a "compatible installation" of vida? could you suggest 
> which are the .tar.gz files that we have to download from the OpenEye 
> website in order to use ROCS and VIDA?
>
> I have asked this also to support]*[eyesopen.com 
> <mailto:support%5D*%5Beyesopen.com> but they have replyed me that 
> their software is not supported in Ubuntu ...
>
> With many thanks in advances for your help and time
>
> Yours sincerely
>
> Gerard
>


From owner-chemistry@ccl.net Thu Oct 29 10:49:00 2009
From: "Morad El-Hendawy m80elhendawy|a|yahoo.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: Colleced AMBER Test jobs file
Message-Id: <-40555-091029101647-25519-CB9+/DfIXsd2Xp7TIVFGDw-*-server.ccl.net>
X-Original-From: Morad El-Hendawy <m80elhendawy-$-yahoo.com>
Content-Type: multipart/mixed; boundary="0-16533782-1256822195=:41953"
Date: Thu, 29 Oct 2009 06:16:35 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Morad El-Hendawy [m80elhendawy-*-yahoo.com]
--0-16533782-1256822195=:41953
Content-Type: multipart/alternative; boundary="0-70344222-1256822195=:41953"

--0-70344222-1256822195=:41953
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Dear Collegues,
Here is an attache file,=A0 a collection of AMBER job tests. This may be be=
nfit for you especially for bigginers. It may help you to compare among the=
 role of different keywords, molecular specifications, partial charges.
Best regards
***************************************************************************=
***********************Morad M. El-HendawyPh.D. Candidate,Solar Energy Conv=
ersion Strategic Research ClusterUCD School of Chemical and Biochemical Pro=
cessEngineering and Material Science CentreNational University of Ireland, =
Dublin [University College Dublin (UCD)]Belfield Dublin 4IrelandLab. No: 31=
9Mobile: =A0 =A0+3530870647869=A0=A0=A0Fax: +35317161177Email: Morad.Elhend=
awy^UCD.ie*****************************************************************=
*********************************=A0If you want a happy life, do four thing=
s:=A01- Contemplate and be thankful,
2- The past is gone forever,
3- Today all that you have,
4- Leave the future alone until it come.=A0********************************=
***************************************************************************=
********=0A=0A=0A      
--0-70344222-1256822195=:41953
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><br>Dear Collegues,<br>Here is an attache fil=
e,&nbsp; a collection of AMBER job tests. This may be benfit for you especi=
ally for bigginers. It may help you to compare among the role of different =
keywords, molecular specifications, partial charges.<br>Best regards<br><di=
v><strong><font color=3D"#00407f"><font style=3D"background-color: rgb(230,=
 230, 230);" size=3D"4" face=3D"arial, helvetica, sans-serif">*************=
***************************************************************************=
**********</font></font></strong></div><div><strong><font color=3D"#00407f"=
><font style=3D"background-color: rgb(230, 230, 230);" face=3D"arial, helve=
tica, sans-serif">Morad M. El-Hendawy</font></font></strong></div><div><str=
ong><font style=3D"background-color: rgb(230, 230, 230);" color=3D"#000000"=
 face=3D"Arial">Ph.D. Candidate,</font></strong></div><div><strong><font st=
yle=3D"background-color:
 rgb(230, 230, 230);" color=3D"#00407f" face=3D"Arial">Solar Energy Convers=
ion Strategic Research Cluster</font></strong></div><div><font style=3D"bac=
kground-color: rgb(230, 230, 230);" color=3D"#000000" face=3D"Arial"><stron=
g>UCD School of Chemical and Biochemical Process</strong></font></div><div>=
<strong><font style=3D"background-color: rgb(230, 230, 230);" color=3D"#004=
07f" face=3D"Arial">Engineering and Material Science Centre</font></strong>=
</div><div><font color=3D"#00407f"><font color=3D"#000000"><font style=3D"b=
ackground-color: rgb(230, 230, 230);"><font face=3D"arial, helvetica, sans-=
serif"><strong>National University of Ireland, Dublin</strong> </font></fon=
t></font></font></div><div><font style=3D"background-color: rgb(230, 230, 2=
30);" color=3D"#00407f" face=3D"Arial"><strong>[University College Dublin (=
UCD)]</strong></font></div><div><strong><font style=3D"background-color: rg=
b(230, 230, 230);" color=3D"#000000" face=3D"Arial">Belfield Dublin
 4</font></strong></div><div><strong><font style=3D"background-color: rgb(2=
30, 230, 230);" color=3D"#00407f" face=3D"Arial">Ireland</font></strong></d=
iv><div><strong><font style=3D"background-color: rgb(230, 230, 230);" color=
=3D"#000000" face=3D"Arial">Lab. No: 319</font></strong></div><div><strong>=
<font color=3D"#00407f" face=3D"Arial"><font style=3D"background-color: rgb=
(230, 230, 230);" color=3D"#000000"><font color=3D"#00407f">Mobile:</font> =
</font><font style=3D"background-color: rgb(230, 230, 230);"></font><font s=
tyle=3D"background-color: rgb(230, 230, 230);"></font><font style=3D"backgr=
ound-color: rgb(230, 230, 230);">&nbsp; &nbsp;+3530870647869&nbsp;&nbsp;&nb=
sp;</font></font></strong><strong><font color=3D"#00407f" face=3D"Arial"></=
font></strong></div><strong><font color=3D"#00407f" face=3D"Arial"></font><=
/strong><div><strong><font style=3D"background-color: rgb(230, 230, 230);" =
color=3D"#000000" face=3D"Arial">Fax: +35317161177</font></strong></div><di=
v><strong><font color=3D"#00407f"
 face=3D"Arial"><font style=3D"background-color: rgb(230, 230, 230);">Email=
: </font><a rel=3D"nofollow" target=3D"_blank" href=3D"mailto:Morad.Elhenda=
wy^UCD.ie"><font style=3D"background-color: rgb(230, 230, 230);">Morad.Elhe=
ndawy^UCD.ie</font></a></font></strong></div><div><strong><font style=3D"ba=
ckground-color: rgb(230, 230, 230);" size=3D"4" color=3D"#00407f" face=3D"A=
rial">*********************************************************************=
*****************************</font></strong></div><div><strong><font style=
=3D"background-color: rgb(230, 230, 230);" color=3D"#00407f"></font></stron=
g><font size=3D"4">&nbsp;</font><strong><font style=3D"background-color: rg=
b(255, 128, 255);" size=3D"4" color=3D"#000000" face=3D"arial, helvetica, s=
ans-serif">If you want a happy life, do four things:</font></strong></div><=
div><strong><font color=3D"#00407f"><font style=3D"background-color: rgb(23=
0, 230, 230);"></font></font></strong><font size=3D"4" face=3D"arial, helve=
tica,
 sans-serif">&nbsp;</font></div><div><strong><font color=3D"#00407f"><font =
style=3D"background-color: rgb(230, 230, 230);" color=3D"#373e68" face=3D"a=
rial, helvetica, sans-serif">1- Contemplate and be thankful,<br></font><fon=
t face=3D"arial, helvetica, sans-serif"><font style=3D"background-color: rg=
b(230, 230, 230);"><font color=3D"#373e68">2- The past is gone forever,<br>=
3- Today all that you have,<br>4- Leave the future alone until it come.</fo=
nt>&nbsp;</font></font></font></strong></div><div><strong><font style=3D"ba=
ckground-color: rgb(230, 230, 230);" color=3D"#00407f" face=3D"Arial">*****=
***************************************************************************=
***********************************</font></strong></div><img alt=3D""><str=
ong></strong></td></tr></table><br>=0A=0A      
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--0-16533782-1256822195=:41953--


From owner-chemistry@ccl.net Thu Oct 29 12:05:00 2009
From: "Morad El-Hendawy m80elhendawy ~~ yahoo.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: explanation
Message-Id: <-40556-091029120350-20365-iOp7WLDunAWG1bU8y4Dvig-*-server.ccl.net>
X-Original-From: Morad El-Hendawy <m80elhendawy[#]yahoo.com>
Content-Type: multipart/alternative; boundary="0-334888108-1256832218=:84695"
Date: Thu, 29 Oct 2009 09:03:38 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Morad El-Hendawy [m80elhendawy!^!yahoo.com]
--0-334888108-1256832218=:84695
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

Hey Basma,
Firstly, polar hydrogen atoms,=0Aare those attached to N, O & S atoms and t=
he non-polar ones, are=0Athose attached to carbon atoms. Secondly, typicall=
y most=0Acrystallographic experiments do not see=A0 hydrogen atoms, but wit=
h high=0Aresolution instrument, H-atoms can be seen. Beside that, NMR techn=
ique=0Asees all H-atoms. So, you have to check which=A0 method determined t=
he=0Ainterested protein, NMR, X-ray or other. Afterwards, investigate your=
=0APDB file and check the presence of H-atoms. Usually, PDB structure=0Agen=
erated from X-ray do not include hydrogen atom,=0Aso these are added by sui=
table program like gaussview, VMD,, etc. In=0Asome cases, the program added=
 the hydrogen atoms wrongly to ligand,=0Ahence you can delete the hydrogen =
atoms of the wrong potions then add=0Athem manually.=20
Best regards,


***************************************************************************=
***********************Morad M. El-Hendawy*********************************=
*****************************************************************=A0If you =
want a happy life, do four things:=A01- Contemplate and be thankful,
2- The past is gone forever,
3- Today all that you have,
4- Leave the future alone until it come.=A0********************************=
***************************************************************************=
********

--- On Thu, 10/29/09, Basma Ghazal basmaghazal{:}ymail.com <owner-chemistry=
,ccl.net> wrote:

> From: Basma Ghazal basmaghazal{:}ymail.com <owner-chemistry,ccl.net>
Subject: CCL: explanation
To: "El-Hendawy, Morad Metwally " <m80elhendawy,yahoo.com>
Date: Thursday, October 29, 2009, 1:17 PM

Dear CClers:=0AI want to know why we delete hydrogen atoms from the pdb str=
ucture and then add the polar onewhen we prepare it for docking?=0AWhat is =
the different between the polar and non polar.=0AI will be appreciate if an=
y one reply.=0AThanks,
=0A=0A=0A=0A      =0A=0A=0A      
--0-334888108-1256832218=:84695
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;">Hey Basma,<br>Firstly, polar <span style=3D"b=
order-bottom: 1px dashed rgb(0, 102, 204); background: transparent none rep=
eat scroll 0% 0%; cursor: pointer; -moz-background-clip: border; -moz-backg=
round-origin: padding; -moz-background-inline-policy: continuous;" class=3D=
"yshortcuts" id=3D"lw_1256832162_0">hydrogen atoms</span>,=0Aare those atta=
ched to N, O &amp; S atoms and the non-polar ones, are=0Athose attached to =
carbon atoms. Secondly, typically most=0Acrystallographic experiments do no=
t see&nbsp; hydrogen atoms, but with high=0Aresolution instrument, H-atoms =
can be seen. Beside that, NMR technique=0Asees all H-atoms. So, you have to=
 check which&nbsp; method determined the=0Ainterested protein, NMR, X-ray o=
r other. Afterwards, investigate your=0APDB file and check the presence of =
H-atoms. Usually, PDB structure=0Agenerated from X-ray do not include <span=
 class=3D"yshortcuts" id=3D"lw_1256832162_1">hydrogen atom</span>,=0Aso the=
se are added by suitable program like gaussview, VMD,, etc. In=0Asome cases=
, the program added the hydrogen atoms wrongly to ligand,=0Ahence you can d=
elete the hydrogen atoms of the wrong potions then add=0Athem manually. <br=
>Best regards,<br><br><div><br><strong><font color=3D"#00407f"><font style=
=3D"background-color: rgb(230, 230, 230);" face=3D"arial, helvetica, sans-s=
erif" size=3D"4">**********************************************************=
****************************************</font></font></strong></div><div><=
strong><font color=3D"#00407f"><font style=3D"background-color: rgb(230, 23=
0, 230);" face=3D"arial, helvetica, sans-serif">Morad M. El-Hendawy</font><=
/font></strong></div><div><strong><font style=3D"background-color: rgb(230,=
 230, 230);" face=3D"Arial" size=3D"4" color=3D"#00407f">******************=
***************************************************************************=
*****</font></strong></div><div><strong><font style=3D"background-color: rg=
b(230, 230, 230);" color=3D"#00407f"></font></strong><font size=3D"4">&nbsp=
;</font><strong><font style=3D"background-color: rgb(255, 128, 255);" face=
=3D"arial, helvetica, sans-serif" size=3D"4" color=3D"#000000">If you want =
a happy life,
 do four things:</font></strong></div><div><strong><font color=3D"#00407f">=
<font style=3D"background-color: rgb(230, 230, 230);"></font></font></stron=
g><font face=3D"arial, helvetica, sans-serif" size=3D"4">&nbsp;</font></div=
><div><strong><font color=3D"#00407f"><font style=3D"background-color: rgb(=
230, 230, 230);" face=3D"arial, helvetica, sans-serif" color=3D"#373e68">1-=
 Contemplate and be thankful,<br></font><font face=3D"arial, helvetica, san=
s-serif"><font style=3D"background-color: rgb(230, 230, 230);"><font color=
=3D"#373e68">2- The past is gone forever,<br>3- Today all that you have,<br=
>4- Leave the future alone until it come.</font>&nbsp;</font></font></font>=
</strong></div><div><strong><font style=3D"background-color: rgb(230, 230, =
230);" face=3D"Arial" color=3D"#00407f">***********************************=
***************************************************************************=
*****</font></strong></div><img alt=3D""><strong></strong><br><br>--- On <b=
>Thu, 10/29/09, Basma
 Ghazal basmaghazal{:}ymail.com <i>&lt;owner-chemistry,ccl.net&gt;</i></b> =
wrote:<br><blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); mar=
gin-left: 5px; padding-left: 5px;"><br>From: Basma Ghazal basmaghazal{:}yma=
il.com &lt;owner-chemistry,ccl.net&gt;<br>Subject: CCL: explanation<br>To: =
"El-Hendawy, Morad Metwally " &lt;m80elhendawy,yahoo.com&gt;<br>Dat=
e: Thursday, October 29, 2009, 1:17 PM<br><br><div id=3D"yiv1472389584"><st=
yle type=3D"text/css"><!--#yiv1472389584 DIV {margin:0px;}--></style><div s=
tyle=3D"font-family: tahoma,new york,times,serif; font-size: 14pt;"><p>Dear=
 CClers:</p>=0A<p>I want to know why we delete hydrogen atoms from the pdb =
structure and then add the polar onewhen we prepare it for docking?</p>=0A<=
p>What is the different between the polar and non polar.</p>=0A<p>I will be=
 appreciate if any one reply.</p>=0A<p>Thanks,</p></div><br>=0A=0A=0A=0A   =
   </div></blockquote></td></tr></table><br>=0A=0A=0A=0A      
--0-334888108-1256832218=:84695--


From owner-chemistry@ccl.net Thu Oct 29 12:39:00 2009
From: "Greg Warren greg|a|eyesopen.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?
Message-Id: <-40557-091029113038-8591-0doRIZALcrdAlcOSKjjT9A+*+server.ccl.net>
X-Original-From: Greg Warren <greg!^!eyesopen.com>
Content-Language: en-US
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="iso-8859-1"
Date: Thu, 29 Oct 2009 07:58:57 -0700
MIME-Version: 1.0


Sent to CCL by: Greg Warren [greg _ eyesopen.com]
Gerard,

Vincent's suggestion should work for ROCS.  There is a chance is will not w=
ork for Vida. Another solution is to copy the executable ~/openeye/arch/ver=
sion_downloaded/rocs/version_number/bin/rocs to ~/openeye/bin.  This saves =
you the effort of editing the startup script if you are uncomfortable with =
that.

Greg

-----Original Message-----
> From: owner-chemistry+greg=3D=3Deyesopen.com{:}ccl.net [mailto:owner-chemistr=
y+greg=3D=3Deyesopen.com{:}ccl.net] On Behalf Of Vincent Leroux vincent.lerou=
x^^loria.fr
Sent: Thursday, October 29, 2009 8:13 AM
To: Greg Warren
Subject: CCL: Do ROCS and VIDA (from OpenEye) work with the 64bits version =
of Ubuntu?


Sent to CCL by: Vincent Leroux [vincent.leroux]|[loria.fr]
Hi Gerard,

First, pick up the SLED10-x64 versions.
They work well on my 8.04 64-bit Ubuntu system, this should also be the=20
case on 9.04.

If you still have problems, I suggest editing the uselessly complicated=20
(and definitely not Ubuntu-friendly) program launch script (it should be=20
in openeye/bin/, the actual executable being located in=20
arch/suse-SLED10-x64/program/version/bin/).

Delete / comment out the initializations

ostype=3D"unknown"
osver=3D`uname -r ...`
arch=3D""

then replace by:

ostype=3Dsuse
osver=3DSLED10
arch=3Dx64

then delete / comment out the whole case...esac construct just afterwards.
This will make sure that the script will not hopelessly try to determine=20
the system architecture by itself.

This might do the trick.

Regards,
Vincent Leroux



Gerard Pujadas gerard.pujadas]-[gmail.com a =E9crit :
>
> Dear CCL subscribers,
>
> is any one in the list running ROCS and VIDA (from OpenEye) with the=20
> 64bits version of Ubuntu (I currently have version 9.04 installed on=20
> my computer)?
>
> I have installed in my computer the eon-2.0.1-suse-9.1-x86_64.tar.gz=20
> file and the resulting EON software runs perfectly. Nevertheless, when
> I tried to run the ROCS or VIDA downloaded from the same page that EON=20
> (rocs-2.4.2-suse-9.1-x64.tar.gz and vida-4.0.0-suse-9.1-x64.tar.gz=20
> files, respectively), the next error messages appear:
>
>
> esther]*[nutrigenomica002:~$ vida
>
> ERROR: Unable to find an appropriate installation of vida for
>        this architecture (linux-2.6-x64).
>                               =20
>        Available compatible installations of vida:
>
> which would be a "compatible installation" of vida? could you suggest=20
> which are the .tar.gz files that we have to download from the OpenEye=20
> website in order to use ROCS and VIDA?
>
> I have asked this also to support]*[eyesopen.com=20
> <mailto:support%5D*%5Beyesopen.com> but they have replyed me that=20
> their software is not supported in Ubuntu ...
>
> With many thanks in advances for your help and time
>
> Yours sincerely
>
> Gerard
>



-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Oct 29 13:14:00 2009
From: "Joe Corkery jcorkery:-:eyesopen.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?
Message-Id: <-40558-091029121817-26644-8p3/62L4ZFLtKBdTWfs0pA||server.ccl.net>
X-Original-From: Joe Corkery <jcorkery]_[eyesopen.com>
Content-Language: en-US
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="iso-8859-1"
Date: Thu, 29 Oct 2009 08:47:01 -0700
MIME-Version: 1.0


Sent to CCL by: Joe Corkery [jcorkery : eyesopen.com]
Dear Gerard and Vincent,

While OpenEye does not support Ubuntu, there does exist a mechanism to over=
ride the automatic architecture determination without having to modify the =
start-up script as Vincent noted below. However, please note again that we =
do not support Ubuntu and while some individuals have had success in using =
specific platform installations on other non-supported platforms, OpenEye c=
annot guarantee compatibility across platforms or on non-supported platform=
s and does not provide support for this usage. Furthermore, even if a compa=
tible version is found, there is no guarantee that it will remain compatibl=
e with future versions of the non-supported platform.

All that being said, you can force the start-up script to use a specified a=
rchitecture by setting the OE_ARCH environment variable. In Vincent's case,=
 he could set:

OE_ARCH=3Dsuse-SLED10-x64

which when set forces the 'suse-SLED10-x64' version of the software to be r=
un regardless of what the  current platform actually is. The architecture t=
hat is specified in these environment variables must exactly match the one =
listed in the openeye/arch installation directory.=20

Joe Corkery
OpenEye Scientific Software


-----Original Message-----
> From: owner-chemistry+jcorkery=3D=3Deyesopen.com---ccl.net [mailto:owner-chem=
istry+jcorkery=3D=3Deyesopen.com---ccl.net] On Behalf Of Vincent Leroux vince=
nt.leroux^^loria.fr
Sent: Thursday, October 29, 2009 10:13 AM
To: Joe Corkery
Subject: CCL: Do ROCS and VIDA (from OpenEye) work with the 64bits version =
of Ubuntu?


Sent to CCL by: Vincent Leroux [vincent.leroux]|[loria.fr]
Hi Gerard,

First, pick up the SLED10-x64 versions.
They work well on my 8.04 64-bit Ubuntu system, this should also be the=20
case on 9.04.

If you still have problems, I suggest editing the uselessly complicated=20
(and definitely not Ubuntu-friendly) program launch script (it should be=20
in openeye/bin/, the actual executable being located in=20
arch/suse-SLED10-x64/program/version/bin/).

Delete / comment out the initializations

ostype=3D"unknown"
osver=3D`uname -r ...`
arch=3D""

then replace by:

ostype=3Dsuse
osver=3DSLED10
arch=3Dx64

then delete / comment out the whole case...esac construct just afterwards.
This will make sure that the script will not hopelessly try to determine=20
the system architecture by itself.

This might do the trick.

Regards,
Vincent Leroux



Gerard Pujadas gerard.pujadas]-[gmail.com a =E9crit :
>
> Dear CCL subscribers,
>
> is any one in the list running ROCS and VIDA (from OpenEye) with the=20
> 64bits version of Ubuntu (I currently have version 9.04 installed on=20
> my computer)?
>
> I have installed in my computer the eon-2.0.1-suse-9.1-x86_64.tar.gz=20
> file and the resulting EON software runs perfectly. Nevertheless, when
> I tried to run the ROCS or VIDA downloaded from the same page that EON=20
> (rocs-2.4.2-suse-9.1-x64.tar.gz and vida-4.0.0-suse-9.1-x64.tar.gz=20
> files, respectively), the next error messages appear:
>
>
> esther]*[nutrigenomica002:~$ vida
>
> ERROR: Unable to find an appropriate installation of vida for
>        this architecture (linux-2.6-x64).
>                               =20
>        Available compatible installations of vida:
>
> which would be a "compatible installation" of vida? could you suggest=20
> which are the .tar.gz files that we have to download from the OpenEye=20
> website in order to use ROCS and VIDA?
>
> I have asked this also to support]*[eyesopen.com=20
> <mailto:support%5D*%5Beyesopen.com> but they have replyed me that=20
> their software is not supported in Ubuntu ...
>
> With many thanks in advances for your help and time
>
> Yours sincerely
>
> Gerard
>



-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Oct 29 13:50:00 2009
From: "dewdew zhou dewdew|126.com" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: The l503 error in CBS-QB3 calculation
Message-Id: <-40559-091029122606-29915-Dg3LNOHK+IFLRCrSp3G7HQ~~server.ccl.net>
X-Original-From: "dewdew  zhou" <dewdew_+_126.com>
Date: Thu, 29 Oct 2009 12:26:02 -0400


Sent to CCL by: "dewdew  zhou" [dewdew_._126.com]
Dear all

i have used the CBS-QB3 method to calculate the energy of a complex, and i found that in the CCSD(T)/6-31+G(d') calculation, it is terminated with l502 error. Thaere is no problem of the geometry. Do you know how to fix it? Thanks!


From owner-chemistry@ccl.net Thu Oct 29 20:24:01 2009
From: "David Gallagher gallagher.da|*|gmail.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: Turbomole, new release 6.1
Message-Id: <-40560-091029200006-535-eVSsykVV6fwoYB7zBlM3Ug/a\server.ccl.net>
X-Original-From: David Gallagher <gallagher.da ~~ gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_27150281==.ALT"
Date: Thu, 29 Oct 2009 16:52:53 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da__gmail.com]
--=====================_27150281==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

Turbomole:

A new version (6.1) of Turbomole, one of the fastest and most stable 
quantum chemistry programs, has just been released.  The release 
notes are posted at 
<http://www.cacheresearch.com/turbomole.html>http://www.cacheresearch.com/turbomole.html 


If you wish to try Turbomole, you can download an evaluation copy 
> from the link on the above page.  The user manual and tutorials are 
posted at 
<http://www.cacheresearch.com/turbomole.html#support-t>http://www.cacheresearch.com/turbomole.html#support-t 


Users on support may download the new version now from their existing 
FTP accounts.

David Gallagher
CACheResearch.com 
--=====================_27150281==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
<b>Turbomole:<br><br>
</b>A new version (6.1) of Turbomole, one of the fastest and most stable
quantum chemistry programs, has just been released.&nbsp; The release
notes are posted at
<a href="http://www.cacheresearch.com/turbomole.html">
http://www.cacheresearch.com/turbomole.html</a> <br><br>
If you wish to try Turbomole, you can download an evaluation copy from
the link on the above page.&nbsp; The user manual and tutorials are
posted at
<a href="http://www.cacheresearch.com/turbomole.html#support-t">
http://www.cacheresearch.com/turbomole.html#support-t</a> <br><br>
Users on support may download the new version now from their existing FTP
accounts.&nbsp; <br><br>
David Gallagher<br>
CACheResearch.com</body>
</html>

--=====================_27150281==.ALT--


From owner-chemistry@ccl.net Thu Oct 29 21:27:00 2009
From: "Kave h kaveh01-#-yahoo.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: FormCheck=(MO,Basis) in g09
Message-Id: <-40561-091029202151-1753-v8h6GpsYiuSSHwf9IwvNZQ*_*server.ccl.net>
X-Original-From: "Kave  h" <kaveh01:+:yahoo.com>
Date: Thu, 29 Oct 2009 20:21:45 -0400


Sent to CCL by: "Kave  h" [kaveh01*yahoo.com]
Dear all 
I used this command in g03 "FormCheck=(MO,Basis)"
in g09 output Test.FChk is in different format can I get g03 format Test.FChk from G09 ?
Thank you all