From owner-chemistry@ccl.net Tue Sep 20 07:29:54 2005
From: "CCL" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: using pdb2pqr on a non-standard, non-parametrized residue
Message-Id: <-29240-050920065020-20319-MxPps1ulpfG46D/+2PQnqg]=[server.ccl.net>
X-Original-From: Dr Seth Olsen <s.olsen1]=[uq.edu.au>
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Date: Tue, 20 Sep 2005 20:50:07 +1000
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Sent to CCL by: Dr Seth Olsen [s.olsen1]=[uq.edu.au]

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Hi CCLers,

I must generate likely protonation states for a protein containing a
non-standard residue, and I have decided to use PDB2PQR to perform the
protonation and determine titratable pKa's.  Of course, however, PDB2PQR
chokes on the non-standard, non-parametrized residue.  In order to
generate the full PQR I must determine charges and radii for all atoms
of the non-standard residue.  It would seem that the best way to
generate the charges is to feed a model of the residue through the RESP
charge generation algorithm.  However, I was wondering what is the best
way to determine the radii?  Is there an available software package that
will do this?  

Cheers,

Seth

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Biomolecular Modeling Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1]=[uq.edu.au
Web: www.ccms.uq.edu.au 

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms


From owner-chemistry@ccl.net Tue Sep 20 10:31:43 2005
From: "CCL" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Problem runing job in G03
Message-Id: <-29241-050920101449-24689-yOZkG3mV2ruB3cwK00uDJA-#-server.ccl.net>
X-Original-From: Delwar Hossain <hossaind2004-#-yahoo.com>
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Sent to CCL by: Delwar Hossain [hossaind2004-#-yahoo.com]

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Dear CCLers,
When I run job in Guaussian 03,  the job filed to run with the following error message:
 
Returned from execl,istat=-1,errno=2!
Returned from execl!
Command exited with non-zero status 1
9.09user 1.77system 5:25.68elapsed 3%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (23295major+278624minor)pagefaults 0swaps

I used B3LYP/6-311G** . I would be grateful if anyone help me to identify the problem and suggest me how to solve it.
 
Thank you.
Sincerely yours,
Delwar Hossain
 
 

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 
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<DIV>Dear CCLers,</DIV>
<DIV>When I run job in Guaussian 03, &nbsp;the job filed to run with the following error message:</DIV>
<DIV>&nbsp;</DIV>
<DIV><STRONG>Returned from execl,istat=-1,errno=2!<BR>Returned from execl!<BR>Command exited with non-zero status 1<BR>9.09user 1.77system 5:25.68elapsed 3%CPU (0avgtext+0avgdata 0maxresident)k<BR>0inputs+0outputs (23295major+278624minor)pagefaults 0swaps<BR></STRONG></DIV>
<DIV>I used B3LYP/6-311G** . I would be grateful if anyone help me to identify the problem and suggest me how to solve it.</DIV>
<DIV>&nbsp;</DIV>
<DIV>Thank you.</DIV>
<DIV>Sincerely yours,</DIV>
<DIV>Delwar Hossain</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV><p>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam?  Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com 
--0-1900134403-1127222086=:42979--


From owner-chemistry@ccl.net Tue Sep 20 10:59:38 2005
From: "CCL" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: How to implement electric field ?
Message-Id: <-29242-050920104516-7503-Ju8N1wkn85uAgeQSlgBLVg=-=server.ccl.net>
X-Original-From: <utpal=-=cts.iitkgp.ernet.in>
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Date: Tue, 20 Sep 2005 18:59:00 +051800


Sent to CCL by: [utpal=-=cts.iitkgp.ernet.in]

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I have posted this question few days back but didn't get any response, so postinf it again.

Dear CCL users,
I want to optimize the benzene di thiol [H-S(pC6H4-S-H]
molecule in the presence of electric filed in gaussian G03
software. I want to apply electric field along the X axis
(i.e. along the S-S atom) and also along the axis perpendicular to the plane of the benzene ring. How can I do it? I mean what is the input file for that? I have constructed a input file (see below) for electric filed along the X axis but I am not confirm whether it is along the S-S axis or not? How do I confirm that the filed is along the S-S axis and also perpendicular to the benzene plane? After the optimization in the presence of field, is the S-S axis still along the X axis ? or the plane of the benze ring is perpendicular to the applied field after optimization? 
Thanking you in advance.
With best regards
Utpal

HF/6-31G Field=x+10 Opt=Z-Matrix Nosymm

Field

0 1

C

C 1 B1
C 2 B2 1 A1
C 3 B3 2 A2 1 D1
C 4 B4 3 A3 2 D2
C 1 B5 2 A4 3 D3
H 2 B6 1 A5 6 D4
H 3 B7 2 A6 1 D5
H 5 B8 4 A7 3 D6
H 6 B9 1 A8 2 D7
S 1 B10 6 A9 5 D8
H 11 B11 1 A10 6 D9
S 4 B12 3 A11 2 D10
H 13 B13 4 A12 3 D11

B1 1.39516000
B2 1.39471206
B3 1.39542701
B4 1.39482508
B5 1.39482907
B6 1.09965530
B7 1.09968019
B8 1.09976099
B9 1.09960403
B10 1.78000000
B11 1.31000000
B12 1.78000000
B13 1.31000000
A1 120.00863221
A2 119.99416459
A3 119.99399231
A4 119.99845680
A5 119.98077039
A6 120.01279489
A7 120.01134336
A8 120.00799702
A9 120.00431986
A10 109.50000006
A11 119.98114211
A12 109.50000006
D1 -0.05684321
D2 0.03411439
D3 0.03234809
D4 179.95324796
D5 179.96185208
D6 -180.00000000
D7 179.98917535
D8 -179.97984142
D9 -89.96904840
D10 -179.99643617
D11 90.13393561


___________________________________
IIT Kharagpur Mail v1.0


From owner-chemistry@ccl.net Tue Sep 20 14:49:22 2005
From: "CCL" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: numerical frequency calculation
Message-Id: <-29243-050920144636-24002-CQ7UEtZG1OI/CpHrwIuVfw/a\server.ccl.net>
X-Original-From: Ian Hovell <HOVELL/a\cetem.gov.br>
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Date: Tue, 20 Sep 2005 15:46:34 -0300
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Sent to CCL by: Ian Hovell [HOVELL/a\cetem.gov.br]

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This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

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Dear CCLers,
I stopped a numerical frequency calculation inorder to reboot my =
machine.
The problem is that the calculation won=B4t restart with the keyword
freq=3Dnumer it gives a error on starting the L401 link. I think there =
might
be a problem with the final part of the chk file. Is there a way of
restarting the calulation from an earlier part so that this error is =
written
over and erased from the checkpoint or do I really have to start from
scratch.
=20
TIA
Ian
=20

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charset=3Diso-8859-1">


<META content=3D"MSHTML 6.00.2800.1515" name=3DGENERATOR></HEAD>
<BODY>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D500143818-20092005>Dear=20
CCLers,</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D500143818-20092005>I =
stopped a=20
numerical frequency calculation inorder to reboot my machine. The =
problem is=20
that the calculation won=B4t restart with the keyword freq=3Dnumer it =
gives a error=20
on starting the L401 link. I think there might be a problem with the =
final part=20
of the chk file. Is there a way of restarting the calulation from an =
earlier=20
part so that this error is written over and erased from the checkpoint =
or do I=20
really have to start from scratch.</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D500143818-20092005></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D500143818-20092005>TIA</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Ian</FONT></DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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From owner-chemistry@ccl.net Tue Sep 20 16:21:42 2005
From: "CCL" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: High Raman intensities
Message-Id: <-29245-050920141138-21458-dZAAYqL1AYVv6agw14YamQ * server.ccl.net>
X-Original-From: laurent favaro <laurent.favaro * lpces.u-psud.fr>
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Date: Wed, 21 Sep 2005 00:49:02 +0200
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Sent to CCL by: laurent favaro [laurent.favaro * lpces.u-psud.fr]

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Hi

I am searching for informations on high Raman intensities.
Does anyone heard about theoretical investigation ?
Thank you very much.
Best regards,

L. Favaro


From owner-chemistry@ccl.net Tue Sep 20 16:21:42 2005
From: "CCL" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Problem runing job in G03
Message-Id: <-29244-050920141401-21625-gccLWVHxExQ0RrOUIeEBBw(-)server.ccl.net>
X-Original-From: "Muneerah" <mmogren(-)ksu.edu.sa>
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Sent to CCL by: "Muneerah" [mmogren(-)ksu.edu.sa]

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can you send to me the input to see how can i help you
best wishes
  ----- Original Message -----=20
  From: CCL=20
  To: Mogren, Muneerah =20
  Sent: Tuesday, September 20, 2005 4:14 PM
  Subject: CCL: Problem runing job in G03


  Dear CCLers,
  When I run job in Guaussian 03,  the job filed to run with the =
following error message:

  Returned from execl,istat=3D-1,errno=3D2!
  Returned from execl!
  Command exited with non-zero status 1
  9.09user 1.77system 5:25.68elapsed 3%CPU (0avgtext+0avgdata =
0maxresident)k
  0inputs+0outputs (23295major+278624minor)pagefaults 0swaps

  I used B3LYP/6-311G** . I would be grateful if anyone help me to =
identify the problem and suggest me how to solve it.

  Thank you.
  Sincerely yours,
  Delwar Hossain


  __________________________________________________
  Do You Yahoo!?
  Tired of spam? Yahoo! Mail has the best spam protection around=20
  http://mail.yahoo.com=20

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<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>can you send to me the input to see how =
can i help=20
you</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>best wishes</FONT></DIV>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Downer-chemistry(-)ccl.net =
href=3D"mailto:owner-chemistry(-)ccl.net">CCL</A>=20
  </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Dmmogren(-)ksu.edu.sa=20
  href=3D"mailto:mmogren(-)ksu.edu.sa">Mogren, Muneerah </A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Tuesday, September 20, =
2005 4:14=20
  PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL: Problem runing =
job in=20
  G03</DIV>
  <DIV><BR></DIV>
  <DIV>Dear CCLers,</DIV>
  <DIV>When I run job in Guaussian 03, &nbsp;the job filed to run with =
the=20
  following error message:</DIV>
  <DIV>&nbsp;</DIV>
  <DIV><STRONG>Returned from execl,istat=3D-1,errno=3D2!<BR>Returned =
> from=20
  execl!<BR>Command exited with non-zero status 1<BR>9.09user 1.77system =

  5:25.68elapsed 3%CPU (0avgtext+0avgdata =
0maxresident)k<BR>0inputs+0outputs=20
  (23295major+278624minor)pagefaults 0swaps<BR></STRONG></DIV>
  <DIV>I used B3LYP/6-311G** . I would be grateful if anyone help me to =
identify=20
  the problem and suggest me how to solve it.</DIV>
  <DIV>&nbsp;</DIV>
  <DIV>Thank you.</DIV>
  <DIV>Sincerely yours,</DIV>
  <DIV>Delwar Hossain</DIV>
  <DIV>&nbsp;</DIV>
  <DIV>&nbsp;</DIV>
  <P>__________________________________________________<BR>Do You=20
  Yahoo!?<BR>Tired of spam? Yahoo! Mail has the best spam protection =
around=20
  <BR>http://mail.yahoo.com </P></BLOCKQUOTE></BODY></HTML>

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From owner-chemistry@ccl.net Tue Sep 20 20:52:32 2005
From: "CCL" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: How to implement electric field ?
Message-Id: <-29246-050920182610-25353-Bl9ALGYG3m+t8Zz/bUm/ng[A]server.ccl.net>
X-Original-From: Geoffrey Hutchison <grh25[A]cornell.edu>
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Sent to CCL by: Geoffrey Hutchison [grh25[A]cornell.edu]

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> I want to optimize the benzene di thiol [H-S(pC6H4-S-H] molecule in  
> the presence of electric filed in gaussian G03
> software. I want to apply electric field along the X axis (i.e.  
> along the S-S atom) and also along the axis perpendicular to the  
> plane of the benzene ring. How can I do it?

Your best bet is to input the coordinates in cartesian format, rather  
than z-matrix as you did. If the coordinates are in cartesians, it's  
pretty easy to determine the vector from S to S atom (or to make sure  
your input orientation defines that vector as the x axis).

Gaussian (and just about every other program) will output a table of  
XYZ coordinates as a result of any calculation.

If needed, there are a variety of tools you can use to rotate /  
translate your structure in cartesian coordinates to ensure the  
correct orientation for your purposes. For example:

http://xyz-ops.sourceforge.net/

Cheers,
-Geoff


--
-Dr. Geoffrey Hutchison        <grh25[A]cornell.edu>
Cornell University, Department of Chemistry and Chemical Biology
Abruņa Group                http://abruna.chem.cornell.edu/