From owner-chemistry@ccl.net Wed Jul 10 05:05:01 2013
From: "Shilpi V shilpigre]^[gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: problem with nwchem installation in fedora 14 : Package couldn't found
Message-Id: <-48920-130710025039-2221-yhMg2o2D463VlMjymeTYEg^server.ccl.net>
X-Original-From: "Shilpi  V" <shilpigre|*|gmail.com>
Date: Wed, 10 Jul 2013 02:50:38 -0400


Sent to CCL by: "Shilpi  V" [shilpigre++gmail.com]
Dear members,
I use fedora 14 and downloaded source code file of Nwchem-6.3.revision1-src.2013-05-28.tar.gz and did the following

tar -xvzf Nwchem-6.3.revision1-src.2013-05-28.tar.gz

su
password

yum install nwchem-6.3-src.2013-05-28/
Loaded plugins: langpacks, presto, refresh-packagekit
Adding en_US to language list
Setting up Install Process
No package nwchem-6.3-src.2013-05-28/ available.
Error: Nothing to do


How can I successfully install nwchem??
Please help me with this.

SHILPI


From owner-chemistry@ccl.net Wed Jul 10 05:57:00 2013
From: "jahodovykomplot]^[gmail.com" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL:G: AW: CCL:G: PES Calculation
Message-Id: <-48921-130710050357-2056-m839QZPlYWvEolF0r2bfLQ]-[server.ccl.net>
X-Original-From: <jahodovykomplot(-)gmail.com>
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Date: Wed, 10 Jul 2013 09:03:43 +0000
MIME-Version: 1.0


Sent to CCL by: [jahodovykomplot|a|gmail.com]
Dear Tal,

I have always used fixed step size and the manual page for scan does not mention the possibilty of having a variable step size (but have u tried it?) anyway if u set scan parameters at two or more bond parameters, they will NOT be scanned separately. F.e in one input if u set 2 bonds to get longer with 15 steps of some size, you will get 256 lines of scan - 16 new parameters for each, combined together.

Cheers
J.
----------
Sent via Nokia Email

-----Ursprüngliche Mitteilung-----
Von: Tal Weiss tal.the.white:_:gmail.com <owner-chemistry:+:ccl.net>
To: "Mathauserova, Jana " <mathausj:+:natur.cuni.cz>
Date: Dienstag, 9. Juli 2013 05:32:14 GMT-0400
Subject: CCL:G: PES Calculation


Sent to CCL by: "Tal  Weiss" [tal.the.white#%#gmail.com]
Dear All,

 I am currently using GAUSSIAN 09 to scan for Potential Energy Surfaces. Since 
all the parameters in the z matrix are independent, I can scan one parameter 
(e.g. angle or bond length) and freeze the others. I didn't find however a way 
to scan two depended parameters. For example, Let's say the parameter B1 is 
given by:

B1     1.1         S    10    0.01 

now, I would like that parameter B2 will be B2=2*B1 at each step. (I don't want 
to scan them independently)
Is it possible?

Thanks,
Tal.http://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 Wed Jul 10 06:32:00 2013
From: "Scott Mckechnie jsm78],[cam.ac.uk" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: Repeated single-point energy calculation gives different results
Message-Id: <-48922-130710061930-13413-FEyjc+/TggjDV3qDFEtT0Q : server.ccl.net>
X-Original-From: "Scott  Mckechnie" <jsm78()cam.ac.uk>
Date: Wed, 10 Jul 2013 06:19:29 -0400


Sent to CCL by: "Scott  Mckechnie" [jsm78##cam.ac.uk]
Dear all,

I ran a single-point energy calculation for a molecule with PCM solvent on a gas phase optimized geometry and got an unexpected change in the HOMO energy. I then reran the calculation and got the expected result (difference in the two HOMO energies was ~ 0.4eV). The two calculations were set up with the exact same input geometry and route section:

#p B3LYP/6-31G(d,p) SCRF=(Solvent=n-MethylFormamide-mixture)

Comparing the two output files with the diff command gives the following result:


77c77
<                 10-Jul-2013 
---
>                  8-Jul-2013 
95c95
<  Leave Link    1 at Wed Jul 10 07:11:54 2013, MaxMem=  536870912 cpu:       0.3
---
>  Leave Link    1 at Mon Jul  8 11:55:53 2013, MaxMem=  536870912 cpu:       0.2
298c298
<  Leave Link  101 at Wed Jul 10 07:11:54 2013, MaxMem=  536870912 cpu:       0.3
---
>  Leave Link  101 at Mon Jul  8 11:55:53 2013, MaxMem=  536870912 cpu:       0.2
415c415
<  Leave Link  202 at Wed Jul 10 07:11:55 2013, MaxMem=  536870912 cpu:       0.0
---
>  Leave Link  202 at Mon Jul  8 11:55:53 2013, MaxMem=  536870912 cpu:       0.0
460c460
<  Leave Link  301 at Wed Jul 10 07:11:55 2013, MaxMem=  536870912 cpu:       0.3
---
>  Leave Link  301 at Mon Jul  8 11:55:54 2013, MaxMem=  536870912 cpu:       0.4
471c471
<  Leave Link  302 at Wed Jul 10 07:12:13 2013, MaxMem=  536870912 cpu:      33.0
---
>  Leave Link  302 at Mon Jul  8 11:56:08 2013, MaxMem=  536870912 cpu:      26.3
474c474
<  Leave Link  303 at Wed Jul 10 07:12:14 2013, MaxMem=  536870912 cpu:       0.8
---
>  Leave Link  303 at Mon Jul  8 11:56:09 2013, MaxMem=  536870912 cpu:       1.1
486d485
<  DSYEVD returned Info=        2277 IAlg= 4 N=  1138 NDim=  1138 NE2=      469484 trying DSYEV.
586c585
<  Leave Link  401 at Wed Jul 10 07:12:44 2013, MaxMem=  536870912 cpu:      57.7
---
>  Leave Link  401 at Mon Jul  8 11:56:30 2013, MaxMem=  536870912 cpu:      39.8
608,612c607,611
<  E= -3287.31257045158    
<  DIIS: error= 2.99D-02 at cycle   1 NSaved=   1.
<  NSaved= 1 IEnMin= 1 EnMin= -3287.31257045158     IErMin= 1 ErrMin= 2.99D-02
<  ErrMax= 2.99D-02 EMaxC= 1.00D-01 BMatC= 1.36D+00 BMatP= 1.36D+00
<  IDIUse=3 WtCom= 7.01D-01 WtEn= 2.99D-01
---
>  E= -3287.24015578657    
>  DIIS: error= 2.98D-02 at cycle   1 NSaved=   1.
>  NSaved= 1 IEnMin= 1 EnMin= -3287.24015578657     IErMin= 1 ErrMin= 2.98D-02
>  ErrMax= 2.98D-02 EMaxC= 1.00D-01 BMatC= 1.41D+00 BMatP= 1.41D+00
>  IDIUse=3 WtCom= 7.02D-01 WtEn= 2.98D-01
..

The default Harris guess was used for the initial wavefunction.

Any idea why this could happen?

Best wishes,

Scott


From owner-chemistry@ccl.net Wed Jul 10 07:07:00 2013
From: "kalyan onekalyan ~~ yahoo.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Repeated single-point energy calculation gives different results
Message-Id: <-48923-130710065955-13114-Wb9BgJc06ZG7Ob9JBWct2Q|*|server.ccl.net>
X-Original-From: kalyan <onekalyan-.-yahoo.com>
Content-Type: multipart/alternative; boundary="2164780-559803886-1373453987=:88548"
Date: Wed, 10 Jul 2013 03:59:47 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: kalyan [onekalyan+*+yahoo.com]
--2164780-559803886-1373453987=:88548
Content-Type: text/plain; charset=iso-8859-1
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could you please run your calculation in both gas and PCM again=A0=0APut cm=
d in input section =A0pop=3Dfull gfprint=A0=0A=0Abest regards=0Akalyan kuma=
r dhar=A0=0A=0A=0A=0A>________________________________=0A> From: "Scott Mck=
echnie jsm78],[cam.ac.uk" <owner-chemistry|*|ccl.net>=0A>To: "Dhar, Kalyan ku=
mar " <kalyan.dhar|*|mail.polimi.it> =0A>Sent: Wednesday, July 10, 20=
13 12:19 PM=0A>Subject: CCL: Repeated single-point energy calculation gives=
 different results=0A> =0A>=0A>=0A>Sent to CCL by: "Scott=A0 Mckechnie" [js=
m78##cam.ac.uk]=0A>Dear all,=0A>=0A>I ran a single-point energy calculation=
 for a molecule with PCM solvent on a gas phase optimized geometry and got =
an unexpected change in the HOMO energy. I then reran the calculation and g=
ot the expected result (difference in the two HOMO energies was ~ 0.4eV). T=
he two calculations were set up with the exact same input geometry and rout=
e section:=0A>=0A>#p B3LYP/6-31G(d,p) SCRF=3D(Solvent=3Dn-MethylFormamide-m=
ixture)=0A>=0A>Comparing the two output files with the diff command gives t=
he following result:=0A>=0A>=0A>77c77=0A><=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0  =
10-Jul-2013 =0A>---=0A>>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 8-Jul-2013 =0A>=
95c95=0A><=A0 Leave Link=A0 =A0 1 at Wed Jul 10 07:11:54 2013, MaxMem=3D=A0=
 536870912 cpu:=A0 =A0 =A0  0.3=0A>---=0A>>=A0 Leave Link=A0 =A0 1 at Mon J=
ul=A0 8 11:55:53 2013, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0  0.2=0A>298c2=
98=0A><=A0 Leave Link=A0 101 at Wed Jul 10 07:11:54 2013, MaxMem=3D=A0 5368=
70912 cpu:=A0 =A0 =A0  0.3=0A>---=0A>>=A0 Leave Link=A0 101 at Mon Jul=A0 8=
 11:55:53 2013, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0  0.2=0A>415c415=0A><=
=A0 Leave Link=A0 202 at Wed Jul 10 07:11:55 2013, MaxMem=3D=A0 536870912 c=
pu:=A0 =A0 =A0  0.0=0A>---=0A>>=A0 Leave Link=A0 202 at Mon Jul=A0 8 11:55:=
53 2013, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0  0.0=0A>460c460=0A><=A0 Lea=
ve Link=A0 301 at Wed Jul 10 07:11:55 2013, MaxMem=3D=A0 536870912 cpu:=A0 =
=A0 =A0  0.3=0A>---=0A>>=A0 Leave Link=A0 301 at Mon Jul=A0 8 11:55:54 2013=
, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0  0.4=0A>471c471=0A><=A0 Leave Link=
=A0 302 at Wed Jul 10 07:12:13 2013, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0=
 33.0=0A>---=0A>>=A0 Leave Link=A0 302 at Mon Jul=A0 8 11:56:08 2013, MaxMe=
m=3D=A0 536870912 cpu:=A0 =A0 =A0 26.3=0A>474c474=0A><=A0 Leave Link=A0 303=
 at Wed Jul 10 07:12:14 2013, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0  0.8=
=0A>---=0A>>=A0 Leave Link=A0 303 at Mon Jul=A0 8 11:56:09 2013, MaxMem=3D=
=A0 536870912 cpu:=A0 =A0 =A0  1.1=0A>486d485=0A><=A0 DSYEVD returned Info=
=3D=A0 =A0 =A0 =A0 2277 IAlg=3D 4 N=3D=A0 1138 NDim=3D=A0 1138 NE2=3D=A0 =
=A0 =A0 469484 trying DSYEV.=0A>586c585=0A><=A0 Leave Link=A0 401 at Wed Ju=
l 10 07:12:44 2013, MaxMem=3D=A0 536870912 cpu:=A0 =A0 =A0 57.7=0A>---=0A>>=
=A0 Leave Link=A0 401 at Mon Jul=A0 8 11:56:30 2013, MaxMem=3D=A0 536870912=
 cpu:=A0 =A0 =A0 39.8=0A>608,612c607,611=0A><=A0 E=3D -3287.31257045158=A0 =
=A0 =0A><=A0 DIIS: error=3D 2.99D-02 at cycle=A0  1 NSaved=3D=A0  1.=0A><=
=A0 NSaved=3D 1 IEnMin=3D 1 EnMin=3D -3287.31257045158=A0 =A0  IErMin=3D 1 =
ErrMin=3D 2.99D-02=0A><=A0 ErrMax=3D 2.99D-02 EMaxC=3D 1.00D-01 BMatC=3D 1.=
36D+00 BMatP=3D 1.36D+00=0A><=A0 IDIUse=3D3 WtCom=3D 7.01D-01 WtEn=3D 2.99D=
-01=0A>---=0A>>=A0 E=3D -3287.24015578657=A0 =A0 =0A>>=A0 DIIS: error=3D 2.=
98D-02 at cycle=A0  1 NSaved=3D=A0  1.=0A>>=A0 NSaved=3D 1 IEnMin=3D 1 EnMi=
n=3D -3287.24015578657=A0 =A0  IErMin=3D 1 ErrMin=3D 2.98D-02=0A>>=A0 ErrMa=
x=3D 2.98D-02 EMaxC=3D 1.00D-01 BMatC=3D 1.41D+00 BMatP=3D 1.41D+00=0A>>=A0=
 IDIUse=3D3 WtCom=3D 7.02D-01 WtEn=3D 2.98D-01=0A>..=0A>=0A>The default Har=
ris guess was used for the initial wavefunction.=0A>=0A>Any idea why this c=
ould happen?=0A>=0A>Best wishes,=0A>=0A>Scott=0A>=0A>=0A>=0A>-=3D This is a=
utomatically added to each message by the mailing script =3D-=0A>To recover=
 the email address of the author of the message, please change=0A>the stran=
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STRY|*|ccl.net or use:=0A>=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl=
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
mes new roman, new york, times, serif;font-size:10pt"><div><span>could you =
please run your calculation in both gas and PCM again&nbsp;</span></div><di=
v style=3D"color: rgb(0, 0, 0); font-size: 13px; font-family: 'times new ro=
man', 'new york', times, serif; background-color: transparent; font-style: =
normal;">Put cmd in input section &nbsp;pop=3Dfull gfprint&nbsp;</div><div =
style=3D"color: rgb(0, 0, 0); font-size: 13px; font-family: 'times new roma=
n', 'new york', times, serif; background-color: transparent; font-style: no=
rmal;"><br></div><div style=3D"color: rgb(0, 0, 0); font-size: 13px; font-f=
amily: 'times new roman', 'new york', times, serif; background-color: trans=
parent; font-style: normal;">best regards</div><div style=3D"color: rgb(0, =
0, 0); font-size: 13px; font-family: 'times new roman', 'new york', times, =
serif; background-color: transparent; font-style: normal;">kalyan kumar
 dhar&nbsp;</div><div><br><blockquote style=3D"border-left: 2px solid rgb(1=
6, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;">  <div =
style=3D"font-family: 'times new roman', 'new york', times, serif; font-siz=
e: 10pt;"> <div style=3D"font-family: 'times new roman', 'new york', times,=
 serif; font-size: 12pt;"> <div dir=3D"ltr"> <hr size=3D"1">  <font size=3D=
"2" face=3D"Arial"> <b><span style=3D"font-weight:bold;">From:</span></b> "=
Scott Mckechnie jsm78],[cam.ac.uk" &lt;owner-chemistry|*|ccl.net&gt;<br> <b><=
span style=3D"font-weight: bold;">To:</span></b> "Dhar, Kalyan kumar -id#4i=
m-" &lt;kalyan.dhar|*|mail.polimi.it&gt; <br> <b><span style=3D"font-weight: =
bold;">Sent:</span></b> Wednesday, July 10, 2013 12:19 PM<br> <b><span styl=
e=3D"font-weight: bold;">Subject:</span></b> CCL: Repeated single-point ene=
rgy calculation gives different results<br> </font> </div> <div class=3D"y_=
msg_container"><br><br>Sent to CCL by: "Scott&nbsp; Mckechnie" [jsm78##cam.=
ac.uk]<br>Dear
 all,<br><br>I ran a single-point energy calculation for a molecule with PC=
M solvent on a gas phase optimized geometry and got an unexpected change in=
 the HOMO energy. I then reran the calculation and got the expected result =
(difference in the two HOMO energies was ~ 0.4eV). The two calculations wer=
e set up with the exact same input geometry and route section:<br><br>#p B3=
LYP/6-31G(d,p) SCRF=3D(Solvent=3Dn-MethylFormamide-mixture)<br><br>Comparin=
g the two output files with the diff command gives the following result:<br=
><br><br>77c77<br>&lt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbs=
p;  10-Jul-2013 <br>---<br>&gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &n=
bsp; &nbsp; &nbsp; 8-Jul-2013 <br>95c95<br>&lt;&nbsp; Leave Link&nbsp; &nbs=
p; 1 at Wed Jul 10 07:11:54 2013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbs=
p; &nbsp;  0.3<br>---<br>&gt;&nbsp; Leave Link&nbsp; &nbsp; 1 at Mon Jul&nb=
sp; 8 11:55:53 2013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp;=20
 0.2<br>298c298<br>&lt;&nbsp; Leave Link&nbsp; 101 at Wed Jul 10 07:11:54 2=
013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp;  0.3<br>---<br>&gt;=
&nbsp; Leave Link&nbsp; 101 at Mon Jul&nbsp; 8 11:55:53 2013, MaxMem=3D&nbs=
p; 536870912 cpu:&nbsp; &nbsp; &nbsp;  0.2<br>415c415<br>&lt;&nbsp; Leave L=
ink&nbsp; 202 at Wed Jul 10 07:11:55 2013, MaxMem=3D&nbsp; 536870912 cpu:&n=
bsp; &nbsp; &nbsp;  0.0<br>---<br>&gt;&nbsp; Leave Link&nbsp; 202 at Mon Ju=
l&nbsp; 8 11:55:53 2013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp;=
  0.0<br>460c460<br>&lt;&nbsp; Leave Link&nbsp; 301 at Wed Jul 10 07:11:55 =
2013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp;  0.3<br>---<br>&gt=
;&nbsp; Leave Link&nbsp; 301 at Mon Jul&nbsp; 8 11:55:54 2013, MaxMem=3D&nb=
sp; 536870912 cpu:&nbsp; &nbsp; &nbsp;  0.4<br>471c471<br>&lt;&nbsp; Leave =
Link&nbsp; 302 at Wed Jul 10 07:12:13 2013, MaxMem=3D&nbsp; 536870912 cpu:&=
nbsp; &nbsp; &nbsp; 33.0<br>---<br>&gt;&nbsp; Leave Link&nbsp; 302 at Mon
 Jul&nbsp; 8 11:56:08 2013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nb=
sp; 26.3<br>474c474<br>&lt;&nbsp; Leave Link&nbsp; 303 at Wed Jul 10 07:12:=
14 2013, MaxMem=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp;  0.8<br>---<br>=
&gt;&nbsp; Leave Link&nbsp; 303 at Mon Jul&nbsp; 8 11:56:09 2013, MaxMem=3D=
&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp;  1.1<br>486d485<br>&lt;&nbsp; DSY=
EVD returned Info=3D&nbsp; &nbsp; &nbsp; &nbsp; 2277 IAlg=3D 4 N=3D&nbsp; 1=
138 NDim=3D&nbsp; 1138 NE2=3D&nbsp; &nbsp; &nbsp; 469484 trying DSYEV.<br>5=
86c585<br>&lt;&nbsp; Leave Link&nbsp; 401 at Wed Jul 10 07:12:44 2013, MaxM=
em=3D&nbsp; 536870912 cpu:&nbsp; &nbsp; &nbsp; 57.7<br>---<br>&gt;&nbsp; Le=
ave Link&nbsp; 401 at Mon Jul&nbsp; 8 11:56:30 2013, MaxMem=3D&nbsp; 536870=
912 cpu:&nbsp; &nbsp; &nbsp; 39.8<br>608,612c607,611<br>&lt;&nbsp; E=3D -32=
87.31257045158&nbsp; &nbsp; <br>&lt;&nbsp; DIIS: error=3D 2.99D-02 at cycle=
&nbsp;  1 NSaved=3D&nbsp;  1.<br>&lt;&nbsp; NSaved=3D 1 IEnMin=3D 1 EnMin=
=3D -3287.31257045158&nbsp;
 &nbsp;  IErMin=3D 1 ErrMin=3D 2.99D-02<br>&lt;&nbsp; ErrMax=3D 2.99D-02 EM=
axC=3D 1.00D-01 BMatC=3D 1.36D+00 BMatP=3D 1.36D+00<br>&lt;&nbsp; IDIUse=3D=
3 WtCom=3D 7.01D-01 WtEn=3D 2.99D-01<br>---<br>&gt;&nbsp; E=3D -3287.240155=
78657&nbsp; &nbsp; <br>&gt;&nbsp; DIIS: error=3D 2.98D-02 at cycle&nbsp;  1=
 NSaved=3D&nbsp;  1.<br>&gt;&nbsp; NSaved=3D 1 IEnMin=3D 1 EnMin=3D -3287.2=
4015578657&nbsp; &nbsp;  IErMin=3D 1 ErrMin=3D 2.98D-02<br>&gt;&nbsp; ErrMa=
x=3D 2.98D-02 EMaxC=3D 1.00D-01 BMatC=3D 1.41D+00 BMatP=3D 1.41D+00<br>&gt;=
&nbsp; IDIUse=3D3 WtCom=3D 7.02D-01 WtEn=3D 2.98D-01<br>..<br><br>The defau=
lt Harris guess was used for the initial wavefunction.<br><br>Any idea why =
this could happen?<br><br>Best wishes,<br><br>Scott<br><br><br><br>-=3D Thi=
s is automatically added to each message by the mailing script =3D-<br>To r=
ecover the email address of the author of the message, please change<br>the=
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--2164780-559803886-1373453987=:88548--


From owner-chemistry@ccl.net Wed Jul 10 07:52:00 2013
From: "kalyan onekalyan|*|yahoo.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: AW: CCL:G: PES Calculation
Message-Id: <-48924-130710065755-11129-brVKYB9LK4i9T6Vu71IvQQ- -server.ccl.net>
X-Original-From: kalyan <onekalyan%yahoo.com>
Content-Type: multipart/alternative; boundary="1524547028-7088520-1373453864=:61519"
Date: Wed, 10 Jul 2013 03:57:44 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: kalyan [onekalyan()yahoo.com]
--1524547028-7088520-1373453864=:61519
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=0A=0AB1=A0 =A0 1.1=A0 =A0 =A0 =A0 S=A0 =A0 10=A0 =A0 0.01=0Ainstead put=0A=
=0AB1=A0 =A0 1.1=A0 =A0 =A0 =A0 S =A0 =A020 =A0 =A00.1 ( for bond let say )=
 try it .=A0=0ANow=A0=0AFreeze the co-ordinate that you want=A0=0Alike if i=
t A1 A2 F 0=A0=0AA1 A2 A3 F 0=A0=0A=0AA1 A2 A3 you choice of atomic distanc=
e or angle you wanna frozen.=A0=0A=0AKind regards=0Akalyan kumar Dhar=A0=0A=
=A0=0A=0A=0A>________________________________=0A> From: jahodovykomplot]^[g=
mail.com <owner-chemistry,,ccl.net>=0A>To: "Dhar, Kalyan kumar " <ka=
lyan.dhar,,mail.polimi.it> =0A>Sent: Wednesday, July 10, 2013 11:03 AM=0A>Su=
bject: CCL:G: AW: CCL:G: PES Calculation=0A> =0A>=0A>=0A>Sent to CCL by: [j=
ahodovykomplot|a|gmail.com]=0A>Dear Tal,=0A>=0A>I have always used fixed st=
ep size and the manual page for scan does not mention the possibilty of hav=
ing a variable step size (but have u tried it?) anyway if u set scan parame=
ters at two or more bond parameters, they will NOT be scanned separately. F=
.e in one input if u set 2 bonds to get longer with 15 steps of some size, =
you will get 256 lines of scan - 16 new parameters for each, combined toget=
her.=0A>=0A>Cheers=0A>J.=0A>----------=0A>Sent via Nokia Email=0A>=0A>-----=
Urspr=FCngliche Mitteilung-----=0A>Von: Tal Weiss tal.the.white:_:gmail.com=
 <owner-chemistry,+,ccl.net>=0A>To: "Mathauserova, Jana " <mathausj,+,natur=
.cuni.cz>=0A>Date: Dienstag, 9. Juli 2013 05:32:14 GMT-0400=0A>Subject: CCL=
:G: PES Calculation=0A>=0A>=0A>Sent to CCL by: "Tal=A0 Weiss" [tal.the.whit=
e#%#gmail.com]=0A>Dear All,=0A>=0A>I am currently using GAUSSIAN 09 to scan=
 for Potential Energy Surfaces. Since =0A>all the parameters in the z matri=
x are independent, I can scan one parameter =0A>(e.g. angle or bond length)=
 and freeze the others. I didn't find however a way =0A>to scan two depende=
d parameters. For example, Let's say the parameter B1 is =0A>given by:=0A>=
=0A>B1=A0 =A0  1.1=A0 =A0 =A0 =A0  S=A0 =A0 10=A0 =A0 0.01 =0A>=0A>now, I w=
ould like that parameter B2 will be B2=3D2*B1 at each step. (I don't want =
=0A>to scan them independently)=0A>Is it possible?=0A>=0A>Thanks,=0A>Tal.ht=
tp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/s=
ub_unsub.shtmlhttp://www.ccl.net/spammers.txt=0A>=0A>=0A>-=3D This is autom=
atically added to each message by the mailing script =3D-=0A>To recover the=
 email address of the author of the message, please change=0A>the strange c=
haracters on the top line to the ,, sign. You can also=0A>look up the X-Orig=
inal-From: line in the mail header.=0A>=0A>E-mail to subscribers: CHEMISTRY=
,,ccl.net or use:=0A>=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage=0A>=0A=0A>=
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e/Unsubscribe: =0A>=A0 =A0 =A0=
=0A>=0A=0A>=0A>Job: =
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nouncements/conferences/=0A>=0A>Search Messages: http://www.ccl.net/chemist=
ry/searchccl/index.shtml=0A>=0A>If your mail bounces from CCL with 5.7.1 er=
ror, check:=0A>=A0 =A0 =A0=0A>=0A>RTFI: htt=
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>
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Content-Transfer-Encoding: quoted-printable

<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
mes new roman, new york, times, serif;font-size:10pt"><div style=3D"font-si=
ze: 10pt;"><span><br></span></div><div style=3D"font-size: 10pt;"><span sty=
le=3D"font-size: 16px;">B1&nbsp; &nbsp; 1.1&nbsp; &nbsp; &nbsp; &nbsp; S&nb=
sp; &nbsp; 10&nbsp; &nbsp; 0.01</span></div><div style=3D"color: rgb(0, 0, =
0); font-size: 16px; font-family: 'times new roman', 'new york', times, ser=
if; background-color: transparent; font-style: normal;">instead put</div><d=
iv style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new r=
oman', 'new york', times, serif; background-color: transparent; font-style:=
 normal;"><br></div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; fon=
t-family: 'times new roman', 'new york', times, serif; background-color: tr=
ansparent; font-style: normal;">B1&nbsp; &nbsp; 1.1&nbsp; &nbsp; &nbsp; &nb=
sp; S &nbsp; &nbsp;20 &nbsp; &nbsp;0.1 ( for bond let say ) try it
 .&nbsp;</div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-fami=
ly: 'times new roman', 'new york', times, serif; background-color: transpar=
ent; font-style: normal;">Now&nbsp;</div><div style=3D"color: rgb(0, 0, 0);=
 font-size: 16px; font-family: 'times new roman', 'new york', times, serif;=
 background-color: transparent; font-style: normal;">Freeze the co-ordinate=
 that you want&nbsp;</div><div style=3D"color: rgb(0, 0, 0); font-size: 16p=
x; font-family: 'times new roman', 'new york', times, serif; background-col=
or: transparent; font-style: normal;">like if it A1 A2 F 0&nbsp;</div><div =
style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roma=
n', 'new york', times, serif; background-color: transparent; font-style: no=
rmal;">A1 A2 A3 F 0&nbsp;</div><div style=3D"color: rgb(0, 0, 0); font-size=
: 16px; font-family: 'times new roman', 'new york', times, serif; backgroun=
d-color: transparent; font-style: normal;"><br></div><div style=3D"color: r=
gb(0,
 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times,=
 serif; background-color: transparent; font-style: normal;">A1 A2 A3 you ch=
oice of atomic distance or angle you wanna frozen.&nbsp;</div><div style=3D=
"color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new=
 york', times, serif; background-color: transparent; font-style: normal;"><=
br></div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: '=
times new roman', 'new york', times, serif; background-color: transparent; =
font-style: normal;">Kind regards</div><div style=3D"color: rgb(0, 0, 0); f=
ont-size: 16px; font-family: 'times new roman', 'new york', times, serif; b=
ackground-color: transparent; font-style: normal;">kalyan kumar Dhar&nbsp;<=
/div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: 'time=
s new roman', 'new york', times, serif; background-color: transparent; font=
-style: normal;">&nbsp;<br><blockquote style=3D"font-size: 10pt;
 border-left-width: 2px; border-left-style: solid; border-left-color: rgb(1=
6, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;">  <div =
style=3D"font-family: 'times new roman', 'new york', times, serif; font-siz=
e: 10pt;"> <div style=3D"font-family: 'times new roman', 'new york', times,=
 serif; font-size: 12pt;"> <div dir=3D"ltr"> <hr size=3D"1">  <font size=3D=
"2" face=3D"Arial"> <b><span style=3D"font-weight:bold;">From:</span></b> j=
ahodovykomplot]^[gmail.com &lt;owner-chemistry,,ccl.net&gt;<br> <b><span sty=
le=3D"font-weight: bold;">To:</span></b> "Dhar, Kalyan kumar " &lt;=
kalyan.dhar,,mail.polimi.it&gt; <br> <b><span style=3D"font-weight: bold;">S=
ent:</span></b> Wednesday, July 10, 2013 11:03 AM<br> <b><span style=3D"fon=
t-weight: bold;">Subject:</span></b> CCL:G: AW: CCL:G: PES Calculation<br> =
</font> </div> <div class=3D"y_msg_container"><br><br>Sent to CCL by: [jaho=
dovykomplot|a|gmail.com]<br>Dear Tal,<br><br>I have always used fixed step =
size and the
 manual page for scan does not mention the possibilty of having a variable =
step size (but have u tried it?) anyway if u set scan parameters at two or =
more bond parameters, they will NOT be scanned separately. F.e in one input=
 if u set 2 bonds to get longer with 15 steps of some size, you will get 25=
6 lines of scan - 16 new parameters for each, combined together.<br><br>Che=
ers<br>J.<br>----------<br>Sent via Nokia Email<br><br>-----Urspr=FCngliche=
 Mitteilung-----<br>Von: Tal Weiss tal.the.white:_:gmail.com &lt;owner-chem=
istry,+,ccl.net&gt;<br>To: "Mathauserova, Jana " &lt;mathausj,+,natur.cuni.=
cz&gt;<br>Date: Dienstag, 9. Juli 2013 05:32:14 GMT-0400<br>Subject: CCL:G:=
 PES Calculation<br><br><br>Sent to CCL by: "Tal&nbsp; Weiss" [tal.the.whit=
e#%#gmail.com]<br>Dear All,<br><br> I am currently using GAUSSIAN 09 to sca=
n for Potential Energy Surfaces. Since <br>all the parameters in the z matr=
ix are independent, I can scan one parameter <br>(e.g. angle or bond
 length) and freeze the others. I didn't find however a way <br>to scan two=
 depended parameters. For example, Let's say the parameter B1 is <br>given =
by:<br><br>B1&nbsp; &nbsp;  1.1&nbsp; &nbsp; &nbsp; &nbsp;  S&nbsp; &nbsp; =
10&nbsp; &nbsp; 0.01 <br><br>now, I would like that parameter B2 will be B2=
=3D2*B1 at each step. (I don't want <br>to scan them independently)<br>Is i=
t possible?<br><br>Thanks,<br>Tal.<a href=3D"http://www.ccl.net/cgi-bin/ccl=
/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl=
.net/spammers.txt" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_cc=
l_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spa=
mmers.txt</a><br><br><br>-=3D This is automatically added to each message b=
y the mailing script =3D-<br>To recover the email address of the author of =
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> </div> </blockquote></div>   </div></body></html>
--1524547028-7088520-1373453864=:61519--


From owner-chemistry@ccl.net Wed Jul 10 10:32:00 2013
From: "Philippe Bourassa philippe.bourassa ~~ uqtr.ca" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: The most recent papers in computational chemistry
Message-Id: <-48925-130710102929-27690-SDvZVsytDiydtjwew10+SA:-:server.ccl.net>
X-Original-From: Philippe Bourassa <philippe.bourassa^_^uqtr.ca>
Content-Type: multipart/alternative; boundary=047d7bd6ac2a7cb22004e1291ae3
Date: Wed, 10 Jul 2013 10:29:21 -0400
MIME-Version: 1.0


Sent to CCL by: Philippe Bourassa [philippe.bourassa _ uqtr.ca]
--047d7bd6ac2a7cb22004e1291ae3
Content-Type: text/plain; charset=ISO-8859-1

www.chemfeeds.com is the one I use. Has pretty much every chemistry journal
out there you can choose from.


2013/7/9 Lucus White lucus.white2000,gmail.com <owner-chemistry . ccl.net>

>
> Sent to CCL by: "Lucus  White" [lucus.white2000[]gmail.com]
> Hi All,
>
> I'm just curious about what the best way is to check the latest papers.
> For instance, I want to see the
> most recent issues and the ASAP papers in the major journals. I normally
> visit the journal websites one
> by one, but is there any better way to do it?
>
> Any suggestions would be appreciated.
>
> Best wishes,
> Lucus
> lucus.white2000,,gmail.com>
>
>

--047d7bd6ac2a7cb22004e1291ae3
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><a href=3D"http://www.chemfeeds.com">www.chemfeeds.com</a>=
 is the one I use. Has pretty much every chemistry journal out there you ca=
n choose from.<br></div><div class=3D"gmail_extra"><br><br><div class=3D"gm=
ail_quote">
2013/7/9 Lucus White lucus.white2000,<a href=3D"http://gmail.com">gmail.com=
</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry . ccl.net" targe=
t=3D"_blank">owner-chemistry . ccl.net</a>&gt;</span><br><blockquote class=3D=
"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding=
-left:1ex">
<br>
Sent to CCL by: &quot;Lucus =A0White&quot; [lucus.white2000[]<a href=3D"htt=
p://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Hi All,<br>
<br>
I&#39;m just curious about what the best way is to check the latest papers.=
 For instance, I want to see the<br>
most recent issues and the ASAP papers in the major journals. I normally vi=
sit the journal websites one<br>
by one, but is there any better way to do it?<br>
<br>
Any suggestions would be appreciated.<br>
<br>
Best wishes,<br>
Lucus<br>
lucus.white2000,,<a href=3D"http://gmail.com" target=3D"_blank">gmail.com</=
a><br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
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get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
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<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
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et/jobs</a><br>
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rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
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tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
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<br<br>
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ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br></div>

--047d7bd6ac2a7cb22004e1291ae3--


From owner-chemistry@ccl.net Wed Jul 10 14:59:00 2013
From: "Van Dam, Hubertus J HubertusJJ.vanDam[#]pnnl.gov" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: problem with nwchem installation in fedora 14 : Package couldn't found
Message-Id: <-48926-130710145208-22690-bdh1SPRQ2gz2YGCyn0tmhw[#]server.ccl.net>
X-Original-From: "Van Dam, Hubertus J" <HubertusJJ.vanDam]_[pnnl.gov>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
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Date: Wed, 10 Jul 2013 11:52:00 -0700
MIME-Version: 1.0


Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam() pnnl.gov]
Hi Shilpi,

I you want to install NWChem from source code please read the installation instructions (you need to have MPI installed for this to work):

http://www.nwchem-sw.org/index.php/Compiling_NWChem#How-to:_Build_nwchem_script

Alternatively I know that there are a number of people who generate RPMs for NWChem. Please look for a suitable RPM if that is what you want.

Huub van Dam
Pacific Northwest National Laboratory
Tel:  509-372-6441 





-----Original Message-----
> From: owner-chemistry+hubertus.vandam==pnnl.gov%a%ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov%a%ccl.net] On Behalf Of Shilpi V shilpigre]^[gmail.com
Sent: Tuesday, July 09, 2013 11:51 PM
To: Van Dam, Hubertus J
Subject: CCL: problem with nwchem installation in fedora 14 : Package couldn't found


Sent to CCL by: "Shilpi  V" [shilpigre++gmail.com] Dear members, I use fedora 14 and downloaded source code file of Nwchem-6.3.revision1-src.2013-05-28.tar.gz and did the following

tar -xvzf Nwchem-6.3.revision1-src.2013-05-28.tar.gz

su
password

yum install nwchem-6.3-src.2013-05-28/
Loaded plugins: langpacks, presto, refresh-packagekit Adding en_US to language list Setting up Install Process No package nwchem-6.3-src.2013-05-28/ available.
Error: Nothing to do


How can I successfully install nwchem??
Please help me with this.

SHILPIhttp://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 Wed Jul 10 18:58:00 2013
From: "Igor Filippov Contr igor.filippov_+_nih.gov" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: problem with nwchem installation in fedora 14 : Package couldn't found
Message-Id: <-48927-130710094117-19944-3zryq7rk0oc3Cgf8+qRnqA=-=server.ccl.net>
X-Original-From: "Igor Filippov [Contr]" <igor.filippov---nih.gov>
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Date: Wed, 10 Jul 2013 09:40:41 -0400
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Sent to CCL by: "Igor Filippov [Contr]" [igor.filippov|,|nih.gov]
yum will not compile a package from source code.
yum installs binary rpm packages from repositories.
To compile from source code follow the instructions in the distribution,
if any. Usually it involves running ./configure;make;make install,
sometimes cmake ..;make;make install or other - depending on the build
system.

I would highly recommend getting someone knowledgeable to help you.

Igor

On 7/10/2013 2:50 AM, Shilpi V shilpigre]^[gmail.com wrote:
> 
> Sent to CCL by: "Shilpi  V" [shilpigre++gmail.com]
> Dear members,
> I use fedora 14 and downloaded source code file of Nwchem-6.3.revision1-src.2013-05-28.tar.gz and did the following
> 
> tar -xvzf Nwchem-6.3.revision1-src.2013-05-28.tar.gz
> 
> su
> password
> 
> yum install nwchem-6.3-src.2013-05-28/
> Loaded plugins: langpacks, presto, refresh-packagekit
> Adding en_US to language list
> Setting up Install Process
> No package nwchem-6.3-src.2013-05-28/ available.
> Error: Nothing to do
> 
> 
> How can I successfully install nwchem??
> Please help me with this.
> 
> SHILPI> 
> 
> .
>


From owner-chemistry@ccl.net Wed Jul 10 19:34:00 2013
From: "Daniel Cappel daniel.cappel ~ schrodinger.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Tool to generate conformer database for ligand_like molecules
Message-Id: <-48928-130710113656-12022-T74XnrkTPyYOe6E5XTmiHQ[*]server.ccl.net>
X-Original-From: Daniel Cappel <daniel.cappel+*+schrodinger.com>
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Date: Wed, 10 Jul 2013 17:36:29 +0200
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Sent to CCL by: Daniel Cappel [daniel.cappel]-[schrodinger.com]
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Hi Sun,

you may want to try ConfGen (http://schrodinger.com/productpage/14/26/) for
this, which is good in finding bioactive conformations. For more details on
the method please have a look at the respective publication:

http://pubs.acs.org/doi/abs/10.1021/ci100015j

Best, Daniel



Hello Everyone,
>
> I want to achieve all the possible conformations corresponding to the
> minimums on the potential surface of a ligand_like molecule.
>
>  To this end, I firstly need to generate as many as possible conformers
> by rotating the rotatable bonds via some tools or software; Secondly, A
> sifting stage is performed in which the "bad" conformers having unfavorab=
le
> energies are excluded. To ensure that there are no important conformation=
s
> being omitted. the conformer database generated in the first step must
>  be as completed as possible.
>
> Is there any tool or software that can generate completed conformer
> database for ligand_like molecules ?
>
> Thanks !
>
> -Sun
>



--=20
*Daniel Cappel* - Senior Applications Scientist



----------------------------------------------------------------
Sitz der Gesellschaft/Registered Office:
Schr=F6dinger GmbH, Dynamostr. 13, D-68165 Mannheim
Gesch=E4ftsf=FChrer/Managing Director:  Dr. J=F6rg Weiser
Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannheim

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<div dir=3D"ltr"><div class=3D"gmail_extra">Hi Sun,</div><div class=3D"gmai=
l_extra"><br></div><div class=3D"gmail_extra">you may want to try ConfGen (=
<a href=3D"http://schrodinger.com/productpage/14/26/">http://schrodinger.co=
m/productpage/14/26/</a>) for this, which is good in finding bioactive conf=
ormations. For more details on the method please have a look at the respect=
ive publication:</div>

<div class=3D"gmail_extra"><br></div><div class=3D"gmail_extra"><a href=3D"=
http://pubs.acs.org/doi/abs/10.1021/ci100015j">http://pubs.acs.org/doi/abs/=
10.1021/ci100015j</a><br></div><div class=3D"gmail_extra"><br></div><div cl=
ass=3D"gmail_extra">

Best, Daniel</div><div class=3D"gmail_extra"><br></div><div class=3D"gmail_=
extra"><br><div class=3D"gmail_quote"><br><blockquote class=3D"gmail_quote"=
 style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:=
rgb(204,204,204);border-left-style:solid;padding-left:1ex">

<div dir=3D"ltr">Hello Everyone,
<div><br><div>I want to achieve all the possible conformations correspondin=
g to the minimums on the potential surface of a <span class=3D"">ligand_lik=
e</span> molecule.</div><div><br></div><div>=A0To this end, I firstly need =
to <span class=3D"">generate</span> as many as possible conformers by rotat=
ing the rotatable bonds via some tools or software; Secondly, A sifting sta=
ge is performed in which the &quot;bad&quot; conformers having unfavorable =
energies are excluded.
 To ensure that there are no important conformations being omitted. the <sp=
an class=3D"">conformer</span> <span class=3D"">database</span> generated i=
n the first step must =A0be as completed as possible.=A0</div><div><br></di=
v><div>

Is there any <span class=3D"">tool</span> or software that can <span class=
=3D"">generate</span> completed <span class=3D"">conformer</span> <span cla=
ss=3D"">database</span> for <span class=3D"">ligand_like</span> <span class=
=3D"">molecules</span> ?</div>

</div><div><br></div><div>Thanks !</div><div><br></div><div>-Sun</div></div=
></blockquote></div><br><br clear=3D"all"><div><br></div>-- <br><div dir=3D=
"ltr"><b>Daniel Cappel</b><font color=3D"#000000">=A0-=A0Senior Application=
s Scientist</font><div>

<br></div><div><img src=3D"http://drqqf88j5s1fu.cloudfront.net/Schrodinger_=
logo_medium-size.png" width=3D"96" height=3D"16"><br></div><div><font color=
=3D"#000000"><br></font></div><div><font size=3D"1" color=3D"#999999">-----=
-----------------------------------------------------------<br>

Sitz der Gesellschaft/Registered Office:<br>Schr=F6dinger GmbH, Dynamostr. =
13, D-68165 Mannheim<br>Gesch=E4ftsf=FChrer/Managing Director: =A0Dr. J=F6r=
g Weiser<br>Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannh=
eim</font></div>

</div>
</div></div>

--485b397dd4e3c729cf04e12a0b96--


From owner-chemistry@ccl.net Wed Jul 10 20:09:00 2013
From: "Syeda Hira s.hirabatool+*+ymail.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: How vmd or chimera reads a dcd file
Message-Id: <-48929-130710115905-19554-IcFp0mYj7U8kLFUvkM4qqQ- -server.ccl.net>
X-Original-From: "Syeda  Hira" <s.hirabatool,,ymail.com>
Date: Wed, 10 Jul 2013 11:59:04 -0400


Sent to CCL by: "Syeda  Hira" [s.hirabatool|ymail.com]
I have psf and dcd files.I want to read them using my own script.So I 
want to know how Chimera or VMD reads dcd files.Can you please help me out in 
this regard by providing me some helping material or a script. 

Thank you

Hira Batool
s.hbatool02(~)gmail.com
Student of BS-Bioinformatics
Biosciences Department
COMSATS Institute of Information Technology,Park Road,
Islamabad, PAKISTAN


From owner-chemistry@ccl.net Wed Jul 10 21:11:01 2013
From: "Andrew Orry andy^molsoft.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Tool to generate conformer database for ligand_like molecules
Message-Id: <-48930-130710210925-12183-8qW4va+Oe/qbU1MzDUodJw . server.ccl.net>
X-Original-From: Andrew Orry <andy-,-molsoft.com>
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Date: Wed, 10 Jul 2013 18:09:19 -0700
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Sent to CCL by: Andrew Orry [andy]=[molsoft.com]
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Sun,

If you would like to try MolSoft's 3D conformer generating tool please let
me know and I can send you a key. It is part of our ICM-Chemist-Pro
software http://www.molsoft.com/icm-chemist-pro.html

Some of the key features include:
- Convert 2D chemical sketches (SDF or Mol) and Smiles to 3D.
- Optimize chemicals in the Merck Molecular Force Field.
- Easy browsing of 3D chemicals using a display on/off toggle (browser and
lock) direct from chemical spreadsheet.
- Generate stereoisomers.
- Generate tautomers.
- Convert chemicals to racemic form.
- All functions can be perfermed interactively or in batch mode.

Thanks,
Andy


On Fri, Jul 5, 2013 at 8:01 PM, Bin Sun sunbinxod*gmail.com <
owner-chemistry+*+ccl.net> wrote:

> Hello Everyone,
>
> I want to achieve all the possible conformations corresponding to the
> minimums on the potential surface of a ligand_like molecule.
>
>  To this end, I firstly need to generate as many as possible conformers by
> rotating the rotatable bonds via some tools or software; Secondly, A
> sifting stage is performed in which the "bad" conformers having unfavorable
> energies are excluded. To ensure that there are no important conformations
> being omitted. the conformer database generated in the first step must  be
> as completed as possible.
>
> Is there any tool or software that can generate completed conformer
> database for ligand_like molecules ?
>
> Thanks !
>
> -Sun
>

--047d7b2e47f437e80604e1320be7
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<div dir=3D"ltr">Sun,<div><br></div><div>If you would like to try MolSoft&#=
39;s 3D conformer generating tool please let me know and I can send you a k=
ey. It is part of our ICM-Chemist-Pro software=A0<a href=3D"http://www.mols=
oft.com/icm-chemist-pro.html">http://www.molsoft.com/icm-chemist-pro.html</=
a></div>
<div><br></div><div>Some of the key features include:=A0</div><div><div>- C=
onvert 2D chemical sketches (SDF or Mol) and Smiles to 3D.</div><div>- Opti=
mize chemicals in the Merck Molecular Force Field.</div><div>- Easy browsin=
g of 3D chemicals using a display on/off toggle (browser and lock) direct f=
rom chemical spreadsheet.</div>
<div>- Generate stereoisomers.</div><div>- Generate tautomers.</div><div>- =
Convert chemicals to racemic form.</div><div>- All functions can be perferm=
ed interactively or in batch mode.</div></div><div><br></div><div>Thanks,</=
div>
<div>Andy</div></div><div class=3D"gmail_extra"><br><br><div class=3D"gmail=
_quote">On Fri, Jul 5, 2013 at 8:01 PM, Bin Sun sunbinxod*<a href=3D"http:/=
/gmail.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-che=
mistry+*+ccl.net" target=3D"_blank">owner-chemistry+*+ccl.net</a>&gt;</span> wr=
ote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><div dir=3D"ltr">Hello Everyone,<div><br><di=
v>I want to achieve all the possible conformations corresponding to the min=
imums on the potential surface of a ligand_like molecule.</div>
<div><br></div><div>=A0To this end, I firstly need to generate as many as p=
ossible conformers by rotating the rotatable bonds via some tools or softwa=
re; Secondly, A sifting stage is performed in which the &quot;bad&quot; con=
formers having unfavorable energies are excluded. To ensure that there are =
no important conformations being omitted. the conformer database generated =
in the first step must =A0be as completed as possible.=A0</div>

<div><br></div><div>Is there any tool or software that can generate complet=
ed conformer database for ligand_like molecules ?</div></div><div><br></div=
><div>Thanks !</div><span class=3D"HOEnZb"><font color=3D"#888888"><div><br=
>
</div><div>
-Sun</div></font></span></div>
</blockquote></div><br></div>

--047d7b2e47f437e80604e1320be7--


From owner-chemistry@ccl.net Wed Jul 10 21:46:01 2013
From: "Elaine Meng meng*_*cgl.ucsf.edu" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: How vmd or chimera reads a dcd file
Message-Id: <-48931-130710213206-27980-UNCu3teik5eooyGJba7PJg|server.ccl.net>
X-Original-From: "Elaine  Meng" <meng]![cgl.ucsf.edu>
Date: Wed, 10 Jul 2013 21:32:05 -0400


Sent to CCL by: "Elaine  Meng" [meng%x%cgl.ucsf.edu]
As for Chimera, please see the response to this question on the chimera-users list:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-July/008961.html

Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco