From owner-chemistry@ccl.net Wed Dec  3 05:36:00 2008
From: "Mahmoud Korani Abdel-Latif mkkhedr-*-hotmail.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: XYZ Coordinate Shift (Question and Answers)
Message-Id: <-38228-081203053509-26564-hSeqCdGRdtsQeb5E4Ov3nw\a/server.ccl.net>
X-Original-From: "Mahmoud Korani Abdel-Latif" <mkkhedr]![hotmail.com>
Date: Wed, 3 Dec 2008 05:35:05 -0500


Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr-x-hotmail.com]
Question

Dear CCLer's
I have the XYZ for certain molecule and I need to shift this XYZ to certain values. What I need is that "I need no negative values in the XYZ" because I need that positive coordinates in other calculations.   
 
Is any free program that can do that?
 
Is any script for doing that?
 
Any help to do the above issue will be greatly appreciated.
 
Thanks in advance 
 
Mahmoud
---------------------------

Answers 

#! /bin/bash

shiftx=100.0
shifty=100.0
shiftz=100.0

cat $* |awk '{printf"%4s %10.5f %10.5f %10.5f\n", $1, $2+$shiftx, $3+$shifty, $4+$shiftz;}'

This should shift everything by 100.0 units in every direction.

   
===================================
dr. Marcel Swart

ICREA researcher at
Institut de Qumica Computacional
Universitat de Girona

Parc Cientfic i Tecnolgic
Edifici Jaume Casademont (despatx A-27)
Pic de Peguera 15
17003 Girona
Catalunya (Spain)

tel
+34-972-183240
fax
+34-972-183241
e-mail
marcel.swart!^!icrea.es
marcel.swart!^!udg.edu
web
http://www.icrea.cat/Web/ScientificForm.aspx?key=372
http://iqc.udg.edu/~marcel


--------------

I would ask a crystallographer for help.  They can show you how to
graph your xyz coordinates in the unit cell.  If some parts of a
particular molecule are outside the unit cell, you could just increase
the unit cells dimensions.  
  Of course crystallographers use fractional coordinates.  That's just
x/a, y/b, z/c, etc.  You can easily transform these back to xyz
coordinates with BABEL.
  Regards, Dave Close

------------------

PyMOL does this sort of thing pretty easily:
 
load old_file.pdb
 
alter_state 1, all, (x,y,z)=(x+10,y+2,z+8) 
 
save new_file.pdb
 
This capability has been present for years, so the obsolete free builds
wills suffice:
 
http://delsci.com/rel/099
 
Cheers,
Warren
-----------

A XYZ file is just a text file with a number on the first line (the 
number of atoms) a free format line and then a list of atoms with 
respective XYZ coordinates (4 columns per line).
If you take the coordinates from the file, put them in a spreadsheet 
program (Office, OpenOffice, Gnumeric) and then sum to each element a 
number (one value for all) big enough to make all of them positive, you 
get the desired behavior. Then you copy that back into a xyz file and 
there you go, you have everything positive.
 
This is time consuming but beats learning a new program just to do that.
 
In case you are using Linux, I just cooked up something for you.
awk 'a=10 { if (FNR <= 2) print ; else printf("%2s     %11.6f   %11.6f   
%11.6f \n",$1,$2+a,$3+a,$4+a) }'   <filename>
 
All of this should be done in one line in the shell (from awk to 
<filename>).
<filename> should be the name of your xyz file.
The parameter in beginning (the a=10) is the shift of positions (in this 
case, 10 Angstrom).
Substitute that by any value (integer or not, a decimal number will use 
a . [9.5 for instance]) and you'll get the corresponding shift. The 
shift will be done equally in all dimensions.
 
I only tried this in a couple of files and one operating system but it 
should work on any linux and with any correctly done XYZ file that 
contains only one structure.
 
Best regards,
Daniel Jana

-----------

You could do this very easily (I routinely do) using a spreadsheet
program like Excel. You just have to be careful with tab characters
versus spaces.
 
I copy or open the coordinates in Excel, manipulate the values (e.g. add
10 to every x value), then copy the results into a text file. I then
open the file with Vi and "1,$s/^I/ /g" removes tabs and replaces them
with spaces. Note that "^I" is ctrl-V followed by the tab button (at
least in Windows).
 
Aaron

------------

I would hate to overload you with solutions, but Aten 
(www.projectaten.org, get the Beta version) will also do what you want. 
For example, from the command line one could do:
 
> aten old.xyz -c 'selectall; translate 10 10 10; savemodel xyz new.xyz; 
quit'
 
..to translate all coordinates by 10 Angstroms in each direction. If you 
want all coordinates moved to the 'lower left-hand corner' you can find 
the extreme lower-left-hand coordinate first:
 
> aten old.xyz -c 'real minx,miny,minz; atom i; $minx = 1000.0; $miny = 
1000.0; $minz = 1000.0; for $i; if $i.rx < $minx; $minx = $i.rx; end; if 
$i.ry < $miny; $miny = $i.ry; end; if $i.rz < $minz; $minz = $i.rz; end; 
end; print "Translation is $minx $miny $minz"; selectall; translate 
-$minx -$miny -$minz; savemodel xyz new.xyz; quit'
 
It is also easy with the --batch command to do this for multiple files at 
once.
 
Hope this helps!

---------


Hello, Salam
 
I have seen your question in CCl about XYZ coordination, and I think that you can resolve the problem with Molden, it's a free program http://www.cmbi.ru.nl/molden/molden.html in Linux . But if you work with windows you need Xming-6-9-0-31-setup. If you can't procure this program contact me.
 
  Good luck
------------

Best regards,
Mahmoud


From owner-chemistry@ccl.net Wed Dec  3 07:36:00 2008
From: "Wolf-D.Ihlenfeldt wdi(!)xemistry.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: XYZ Coordinate Shift (Question and Answers)
Message-Id: <-38229-081203072415-21715-DtAHI+NQD6PZAgwq8yEKkg]![server.ccl.net>
X-Original-From: "Wolf-D.Ihlenfeldt" <wdi-.-xemistry.com>
Content-Language: en-us
Content-Transfer-Encoding: quoted-printable
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	charset="iso-8859-1"
Date: Wed, 3 Dec 2008 13:22:58 +0100
MIME-Version: 1.0


Sent to CCL by: "Wolf-D.Ihlenfeldt" [wdi[]xemistry.com]
Yet another solution - here is the CACTVS script:

---
set eh [molfile read "oldmol.xyz"]
lassign [ens get $eh E_XYZEXTENT] xmin xmax ymin ymax zmin zmax
foreach a [ens atoms $eh] v [ens get $eh A_XYZ] {
        atom set $eh $a A_XYZ [vec subtract $v [list $xmin $ymin $zmin]]
}
molfile write "newmol.xyz" $eh
------

Run with the generic interpreter as "csts -f sriptname.tcl" from the =
free
academic toolkit package (www.xemistry.com/academic).

Advantages of this solution:

a) No fixed offset, moves to zero for min. x/y/z coordinate
b) Works automatically with any file format the toolkit can identify,
including xyz, pdb and sdf, and will implicitly convert formats (in case
your input and output formats are different, i.e. xyz->pdb). And you do =
not
need to know the intricacies of the file formats, like the awk solution
below.
c) Works as batch script without further changes. Extending this to =
multiple
files, file name passed as parameter, I/O from/to stdin and stdout,
multi-record files etc. is trivial
d) Supported on all major platforms, including Windows, Linux and =
Solaris.


W. D. Ihlenfeldt
Xemistry GmbH
wdi[*]xemistry.com
---
xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. =
Ihlenfeldt
Address: Auf den Stieden 8, D-35094 Lahntal, Germany
HR Marburg B4713 : Ust/VAT ID DE215316329 : DUNS 34-400-1719
> -----Original Message-----
> From: owner-chemistry+wdi=3D=3Dxemistry.com[*]ccl.net [mailto:owner-
> chemistry+wdi=3D=3Dxemistry.com[*]ccl.net] On Behalf Of Mahmoud Korani =
Abdel-
> Latif mkkhedr-*-hotmail.com
> Sent: Wednesday, December 03, 2008 11:35 AM
> To: Ihlenfeldt, Wolf D 
> Subject: CCL: XYZ Coordinate Shift (Question and Answers)
>=20
>=20
> Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr-x-hotmail.com]
> Question
>=20
> Dear CCLer's
> I have the XYZ for certain molecule and I need to shift this XYZ to
> certain values. What I need is that "I need no negative values in the
> XYZ" because I need that positive coordinates in other calculations.
>=20
> Is any free program that can do that?
>=20
> Is any script for doing that?
>=20
> Any help to do the above issue will be greatly appreciated.
>=20
> Thanks in advance
>=20
> Mahmoud
> ---------------------------
>=20
> Answers
>=20
> #! /bin/bash
>=20
> shiftx=3D100.0
> shifty=3D100.0
> shiftz=3D100.0
>=20
> cat $* |awk '{printf"%4s %10.5f %10.5f %10.5f\n", $1, $2+$shiftx,
> $3+$shifty, $4+$shiftz;}'
>=20
> This should shift everything by 100.0 units in every direction.
>=20
>=20
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> dr. Marcel Swart
>=20
> ICREA researcher at
> Institut de Qumica Computacional
> Universitat de Girona
>=20
> Parc Cientfic i Tecnolgic
> Edifici Jaume Casademont (despatx A-27)
> Pic de Peguera 15
> 17003 Girona
> Catalunya (Spain)
>=20
> tel
> +34-972-183240
> fax
> +34-972-183241
> e-mail
> marcel.swart%%icrea.es
> marcel.swart%%udg.edu
> web
> http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372
> http://iqc.udg.edu/~marcel
>=20
>=20
> --------------
>=20
> I would ask a crystallographer for help.  They can show you how to
> graph your xyz coordinates in the unit cell.  If some parts of a
> particular molecule are outside the unit cell, you could just increase
> the unit cells dimensions.
>   Of course crystallographers use fractional coordinates.  That's just
> x/a, y/b, z/c, etc.  You can easily transform these back to xyz
> coordinates with BABEL.
>   Regards, Dave Close
>=20
> ------------------
>=20
> PyMOL does this sort of thing pretty easily:
>=20
> load old_file.pdb
>=20
> alter_state 1, all, (x,y,z)=3D(x+10,y+2,z+8)
>=20
> save new_file.pdb
>=20
> This capability has been present for years, so the obsolete free =
builds
> wills suffice:
>=20
> http://delsci.com/rel/099
>=20
> Cheers,
> Warren
> -----------
>=20
> A XYZ file is just a text file with a number on the first line (the
> number of atoms) a free format line and then a list of atoms with
> respective XYZ coordinates (4 columns per line).
> If you take the coordinates from the file, put them in a spreadsheet
> program (Office, OpenOffice, Gnumeric) and then sum to each element a
> number (one value for all) big enough to make all of them positive, =
you
> get the desired behavior. Then you copy that back into a xyz file and
> there you go, you have everything positive.
>=20
> This is time consuming but beats learning a new program just to do
> that.
>=20
> In case you are using Linux, I just cooked up something for you.
> awk 'a=3D10 { if (FNR <=3D 2) print ; else printf("%2s     %11.6f   =
%11.6f
> %11.6f \n",$1,$2+a,$3+a,$4+a) }'   <filename>
>=20
> All of this should be done in one line in the shell (from awk to
> <filename>).
> <filename> should be the name of your xyz file.
> The parameter in beginning (the a=3D10) is the shift of positions (in
> this
> case, 10 Angstrom).
> Substitute that by any value (integer or not, a decimal number will =
use
> a . [9.5 for instance]) and you'll get the corresponding shift. The
> shift will be done equally in all dimensions.
>=20
> I only tried this in a couple of files and one operating system but it
> should work on any linux and with any correctly done XYZ file that
> contains only one structure.
>=20
> Best regards,
> Daniel Jana
>=20
> -----------
>=20
> You could do this very easily (I routinely do) using a spreadsheet
> program like Excel. You just have to be careful with tab characters
> versus spaces.
>=20
> I copy or open the coordinates in Excel, manipulate the values (e.g.
> add
> 10 to every x value), then copy the results into a text file. I then
> open the file with Vi and "1,$s/^I/ /g" removes tabs and replaces them
> with spaces. Note that "^I" is ctrl-V followed by the tab button (at
> least in Windows).
>=20
> Aaron
>=20
> ------------
>=20
> I would hate to overload you with solutions, but Aten
> (www.projectaten.org, get the Beta version) will also do what you =
want.
> For example, from the command line one could do:
>=20
> > aten old.xyz -c 'selectall; translate 10 10 10; savemodel xyz
> new.xyz;
> quit'
>=20
> ..to translate all coordinates by 10 Angstroms in each direction. If
> you
> want all coordinates moved to the 'lower left-hand corner' you can =
find
> the extreme lower-left-hand coordinate first:
>=20
> > aten old.xyz -c 'real minx,miny,minz; atom i; $minx =3D 1000.0; =
$miny =3D
> 1000.0; $minz =3D 1000.0; for $i; if $i.rx < $minx; $minx =3D $i.rx; =
end;
> if
> $i.ry < $miny; $miny =3D $i.ry; end; if $i.rz < $minz; $minz =3D =
$i.rz;
> end;
> end; print "Translation is $minx $miny $minz"; selectall; translate
> -$minx -$miny -$minz; savemodel xyz new.xyz; quit'
>=20
> It is also easy with the --batch command to do this for multiple files
> at
> once.
>=20
> Hope this helps!
>=20
> ---------
>=20
>=20
> Hello, Salam
>=20
> I have seen your question in CCl about XYZ coordination, and I think
> that you can resolve the problem with Molden, it's a free program
> http://www.cmbi.ru.nl/molden/molden.html in Linux . But if you work
> with windows you need Xming-6-9-0-31-setup. If you can't procure this
> program contact me.
>=20
>   Good luck
> ------------
>=20
> Best regards,
> Mahmoud
>=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
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
> search)
>=20>=20

From owner-chemistry@ccl.net Wed Dec  3 08:27:01 2008
From: "Vincent Leroux vincent.leroux[#]loria.fr" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Lead optimization
Message-Id: <-38230-081203041616-19720-xBcofD9mlksDMLX78CYRxQ() 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: Wed, 03 Dec 2008 10:15:59 +0100
MIME-Version: 1.0


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

It is obvious that if you have no target structure of any kind, as for 
now you are stuck to ligand-based similarity-driven approaches. In this 
context I would suggest you to so SAR studies ASAP. If you are just 
blindly looking for analogues without having any idea of what to do 
specifically for your target you might lose a lot of time and effort... 
To my knowledge there is no source that will be able to suggest 
automatically relevant chemical substitutions without making use of 
existing SAR or structure data. One substitution might work well for a 
given target/ligand couple, and have the opposite effect on another 
target in the same biological family, and on another ligand on the same 
target. There are many reasons for that, and you have absolutely no 
control over it in the absence of SAR studies and structures of the 
protein-ligand complex... Provided you have enough experimental data to 
start from, one of the greatest benefits of SAR is precisely to 
potentially provide, at a cost generally much lower than for getting 
reliable 3D structures, a clearer view of what you should do or should 
not do to hit your particular target.

As I am specialized in structure-based drug design I might not be the 
most competent to suggest elaborate ligand-based strategies, and which 
tools can provide the best results in that field... But I can give you 
some clues.

Before looking for commercial software you could contact chemical 
suppliers (Akos, Otava, Enamine, etc.) and ask for support in choosing 
compounds to buy. They master the analogue selection techniques and 
programmes well and could help you in choosing a good series of 
analogues, provided they know you will eventually pay for them. But be 
aware that as you have no clue now in what kind of analogues to favor it 
might be needed to buy a good number of compounds (> 1000) to have a 
sensible chance of obtaining novel hits... this might be too expensive 
for an academic lab.

Apart from the commercial software you mentioned (you should ask for an 
OpenEye academic license to have free access to a nice set of good 
tools, if not done already), there are novel techniques that seem to 
perform particularly well for similarity searches. You might find this 
interesting : http://dx.doi.org/10.1021/ci7001507

The ZINC website is a good first place to look for analogue compounds. 
You might try to dump some of your compounds' features in the search 
applet and see what it gives. http://zinc.docking.org/

You should also ask the chemists that made the hit compounds (or ask 
yourself, if you are one such chemist) about what transformations could 
be done to the hits or to any intermediate in their synthesis process. 
Take your time to make the largest possible list of all compounds you 
could virtually synthesize, rank them based on predicted synthesis 
difficulty, mark the ones you have in stock already, and keep this info 
preciously, it might come very useful later.

Eventually if you can plan long-term strategies then I would suggest you 
try to access the structure-based drug design area. You have two 
possibilities for getting a structure of your target :
- Contact molecular modellers, especially those with experience in 
homology modelling, molecular dynamics and docking, in order to build a 
theoretical model. Plan further collaboration with biologists, as any 
model has to be validated by experiments (e.g. mutagenesis) before use.
- If biologists can isolate your target, preferably in complex with one 
of your compounds, then try to find top crystallographers... Once you 
have the structure the modellers can help in getting the most useful 
information for drug design out of it (normal mode analysis, molecular 
dynamics, virtual screening...).

Regards,
VL



Iain Wallace iain.m.wallace/./gmail.com a écrit :
> Hi Vincent,
>
> Thanks for your reply. Basically I work in an academic lab and we 
> would like to purchase some interesting analogues of compounds that we 
> have found. So far, we have no structure and no SAR information.
> I am currently just using a substructure/similarity search to identify 
> compounds. I was wondering if there was anything else out there that 
> might be useful in searching. One thought I had was searching using 
> Bioisosterism, where a chemical group or fragment is replaced by an 
> equivalent group.
> What I have found so far is *S*imilarity *i*n *B*io*I*sosteric *S*pace 
> (SiBIS) from http://www.moltop.com/, and Brood from OpenEye
> The Quantum Isostere Database 
> <http://www.chemistry.manchester.ac.uk/groups/popelier/bioiso.htm>also 
> looks very interesting
>
> Ideally I would like to find a resource that would explain reasons for 
> making particular chemical substitutions or an automatic way of 
> suggesting them
>
> Cheers
>
> Iain
>
> On Tue, Dec 2, 2008 at 11:34 AM, Vincent Leroux vincent.leroux ~~ 
> loria.fr <http://loria.fr> <owner-chemistry]![ccl.net 
> <mailto:owner-chemistry%5D%21%5Bccl.net>> wrote:
>
>
>     Sent to CCL by: Vincent Leroux [vincent.leroux|*|loria.fr
>     <http://loria.fr>]
>     Hi Iain,
>
>     Depends of what you have at this stage. Crystal / NMR structures
>     of complexes, or model structures, or none? Were mutagenesis
>     experiments performed? If there is a target structural model
>     involved, was its conformational space explored, with normal modes
>     analysis / molecular dynamics? You might have biological activity
>     measurements already, but on how much compounds? Are the assays
>     reliable? Were SAR studies done? Were trials of any kind
>     conducted? etc.
>
>     There are numerous lead optimization strategies to choose from,
>     answering the above questions could determine which ones are
>     available to you mostly by eliminating the ones that are not. You
>     might also want to check what amount of effort / manwork you can
>     investigate, what tools are available to you, and in which fields
>     that can be involved in the drug design process (biology, lab
>     chemistry, theoretical chemistry, computer science...).
>
>     You should specify this somewhat so that the related specialists
>     here will be able to help you.
>
>     VL
>
>
>     Iain Wallace iain.m.wallace _ gmail.com <http://gmail.com> a écrit :
>
>         Hi all,
>
>         I was wondering if anybody could give me some basic pointers
>         on lead optimizations.
>         First of all,  is there any (free) software that will propose
>         interesting analogues to make/buy, and give a rationalization
>         for proposing them
>         And also, does any one know of any reviews or books that
>         explains the lead optimization process? I would really like to
>         find something with worked examples
>
>         Thanks a million,
>
>         Cheers
>
>         Iain
>
>


From owner-chemistry@ccl.net Wed Dec  3 09:32:01 2008
From: "Zoran D Matovic zmatovic^-^kg.ac.yu" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: gaussian03 in parallel with unrestricted and PCM modes
Message-Id: <-38231-081203040940-19135-zDEUuVixkcoj6KEypFoDAg{=}server.ccl.net>
X-Original-From: "Zoran D Matovic" <zmatovic*o*kg.ac.yu>
Date: Wed, 3 Dec 2008 04:09:36 -0500


Sent to CCL by: "Zoran D Matovic" [zmatovic=kg.ac.yu]
Hello,

We have a problem with gaussian03 purchased almost five years ago (gaussian03 C02). Since now we used to run g03 using just one cpu. Now we built up 16 cpu beowulf cluster (quad core intel 6600 x 4) and tried to run g03 in parallel using linda7.1. Everything went just fine when ran RHF jobs with no pcm options. however when tried to run: UHF (hf or dft) with or without pcm and any  qm option with PCM solvatation the job hang on after let we say dozen of cycles. At that moment I read just two cpus on main comp and no visible processes on others. Just to mention that we bought g03 for AMD/redhat8.0 and instal it on IntelQuad6600/SciLinux, and there were no bugs except above mentioned. Will You people help us in how to override the prob (do we need to change OS version or...?)

have a nice day
zoran


From owner-chemistry@ccl.net Wed Dec  3 10:07:01 2008
From: "Zoran D Matovic zmatovic_._kg.ac.rs" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL:G: gaussian parallel on unrestricted and PCM modes
Message-Id: <-38232-081203040306-18693-vOKITbvbVlvDirihK9C+4w() server.ccl.net>
X-Original-From: "Zoran D Matovic" <zmatovic-#-kg.ac.rs>
Date: Wed, 3 Dec 2008 04:02:59 -0500


Sent to CCL by: "Zoran D Matovic" [zmatovic a kg.ac.rs]
Hello,

We have a problem with gaussian03 purchased almost five years ago (gaussian03 C02). Since now we used to run g03 using just one cpu. Now we built up 16 cpu beowulf cluster (quad core intel 6600 x 4) and tried to run g03 in parallel using linda7.1. Everything went just fine when ran RHF jobs with no pcm options. however when tried to run: UHF (hf or dft) with or without pcm and any  qm option with PCM solvatation the job hang on after let we say dozen of cycles. At that moment I read just two cpus on main comp and no visible processes on others. Just to mention that we bought g03 for AMD/redhat8.0 and instal it on IntelQuad6600/SciLinux, and there were no bugs except above mentioned. Will You people help us in how to override the prob (do we need to change OS version or...?)

have a nice day
zoran


From owner-chemistry@ccl.net Wed Dec  3 14:53:00 2008
From: "Marcus D. Hanwell marcus=cryos.org" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: GAMESS-US Geometry Optimization Problems With External Electric Fields
Message-Id: <-38233-081202164824-11175-aTpKAAVAUeNvfKwPyi46Iw{=}server.ccl.net>
X-Original-From: "Marcus D. Hanwell" <marcus_+_cryos.org>
Content-Disposition: inline
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  charset="us-ascii"
Date: Tue, 2 Dec 2008 16:15:37 -0500
MIME-Version: 1.0


Sent to CCL by: "Marcus D. Hanwell" [marcus%%cryos.org]

Hi,

I originally posted this on the gamess list, but got no response and was 
hoping someone here might have some ideas. 

I am trying to do some geometry optimizations on organic molecules under an 
external electric field. I was able to optimize the geometry with no field and 
used this geometry as the starting point for the calculation with a field. I 
just added '$EFIELD EVEC(2)=0.001 $END' to the input file and ran a new 
geometry optimization. So I have a control group with,

 $CONTRL COORD=CART UNITS=ANGS RUNTYP=OPTIMIZE $END
 $SYSTEM TIMLIM=99999999999 MEMORY=32000000 $END
 $SCF DIRSCF=.T. FDIFF=.T. NPUNCH=0 $END
 $STATPT NSTEP=150 $END
 $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
 $DFT DFTTYP=B3LYP $END
 $EFIELD EVEC(2)=0.001 $END

With C1 symmetry and nothing more than H, C, N and O in the molecule. I get an 
error message on the first step, ' *** ERROR! THERE ARE NOT 5 OR 6 TRANS/ROT 
MODES NUM T/R=    6 EIGENVALUES=' and below the eigenvalues 'THE CAUSE OF THIS 
IS OFTEN CORRUPTION OF THE HESSIAN'. I tried this with a few different field 
values in EVEC(2) and EVEC(3) (y and z I believe).

Is this the best procedure to employ? Is there something I am missing. Reading 
the manual seems to suggest that the input file should work. I would 
appreciate any tips on how I might get this working. I am using the 
gamess.Apr112008R1.x binary on a Mac OS X Leopard server.

I would appreciate any suggestions on how I might get this working.

Thanks,

Marcus


From owner-chemistry@ccl.net Wed Dec  3 15:41:01 2008
From: "Luis M Sim n lsimon^usal.es" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: translational entropy in solvent
Message-Id: <-38234-081203110835-2873-gwXdYYTne+nM6r235VBnnQ/a\server.ccl.net>
X-Original-From: "Luis M Sim  n" <lsimon]![usal.es>
Date: Wed, 3 Dec 2008 11:08:31 -0500


Sent to CCL by: "Luis M Sim  n" [lsimon|-|usal.es]
Many quantum chemistry packages include implicit solvation models, such as PCM, CPCM, COSMO, 
etc. Nevertheless, even when the optimization was done using any of those solvation models, I have 
observed that the thermal contributions to delta G are calculated assuming that the molecules are in 
the gas phase. Therefore, the translational entropy is overestimated (see, for example, C. Hunter, 
ACIE, 43, 5310-5324, 2004). 

There are models that can estimate this translational entropy in solution (Warshell et al., 
J.Phys.Chem.B, 104, 4578-4584, 2000), but unfortunately these are not straightforward to implement, 
and computational requirements might exceed our possibilities. 

On the other side, I have seen that implicit solvent calculations many times offers a "free solvation 
energy". I do not know if, in that free solvation energy, the translational energy is, somehow, 
evaluated and included, or if it just accounts for cavitation and polarization contributions.

My question is: is it correct to add up the translational estropy calculated assuming gas phase 
behaviour to that free solvation energy? Should not it be more correct if the vibrational or even 
rotational contributions are included in deltaG calculations but translational contribution is excluded? 
Does anyone knows any easy method for, approximately, account for the translational entropy in 
solution, in case that have to be added to the vibrational and rotational contributions?

Sorry if that issue have previously been discussed.


From owner-chemistry@ccl.net Wed Dec  3 20:57:00 2008
From: "Justine A Shaw j-shaw:+:northwestern.edu" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL:G: ONIOM TDDFT charge multiplicity error
Message-Id: <-38235-081203190805-15698-8+TsXXAxM91YzPNeHCEPXQ() server.ccl.net>
X-Original-From: "Justine A Shaw" <j-shaw]![northwestern.edu>
Date: Wed, 3 Dec 2008 19:08:01 -0500


Sent to CCL by: "Justine A Shaw" [j-shaw_+_northwestern.edu]
Dear readers,
I am trying to run an ONIOM TDDFT 2 level calculation and I have run into a difficulty specifying the correct charge/multiplicity for the various levels in the system.  Here is an example of my input file:

%chk=filename.chk             
                                     
%mem=500MB                                                         
# ONIOM(B3LYP/GenECP/Auto TD=(NStates=20):AMBER)                   
# IOp(5/94=0) Geom=Connectivity                                    
# scf=(maxcycle=1000, tight) int=ultrafine                         
                                                                   
title                                                              
                                                                   
3 2 -2 1 5 2                                                     
N-N3-0.13050    -13.013497800    -15.403557100    -17.024036500 L  
H-H-0.20830    -12.530412500    -14.783508400    -16.389442600 L   
H-H-0.20830    -12.646506700    -15.256653500    -17.953609400 L   
H-H-0.20830    -12.809226200    -16.359636100    -16.769526500 L   
...........
etc...

When I run this input file the output immediately states that an incorrect charge/multiplicity is specified.  However,  if I change my charge /multiplicty line to  3 1 -2 1 5 1  the calculation will run for a while then output the following:

 MMInit generated parameter data with length LenPar= 24310.                                          
 Standard basis: Dummy (5D, 7F)                                                                      
 The combination of multiplicity 1 and    91 electrons is impossible.                                
 Error termination via Lnk1e in /usr/common/usg/g03/e1/g03/l301.exe at Sun Nov 23 16:00:31 2008.     
 Job cpu time:  0 days  0 hours  2 minutes 25.2 seconds.                                             
 File lengths (MBytes):  RWF=   2032 Int=      0 D2E=      0 Chk=    376 Scr=      8                 

I do not understand how  it comes up with an electron count of 91? My high level region contains 302 electrons and my low level has thousands of electrons????

Any help on this matter is appreciated!
Thanks in advance,
Justine



-*****************************
Justine Shaw-Condo -Ph.D. Candidate
Ratner and Meade Groups
Department of Chemistry
Northwestern University
Email: j-shaw(_)northwestern.edu
*************************************


From owner-chemistry@ccl.net Wed Dec  3 23:03:01 2008
From: "Kamalakar Jadhav kjadhav[-]vlifesciences.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: Lead optimization
Message-Id: <-38236-081203102818-13790-MFxjwMaRh9khpMkFV4usLw(a)server.ccl.net>
X-Original-From: Kamalakar Jadhav <kjadhav]~[vlifesciences.com>
Content-Type: multipart/alternative;
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Date: Wed, 03 Dec 2008 09:31:57 +0530
MIME-Version: 1.0


Sent to CCL by: Kamalakar Jadhav [kjadhav{}vlifesciences.com]

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Hi Iain
We have developed a new method called GQSAR method. It explains the 
reason for making particular  chemical substitutions or  also suggest 
with simplistic way..GQSAR provides researchers with very important 
site-specific clues for better lead design and also for lead hopping.
For more information Please visit www.VLifeSciences.com

Best Regards,
Kamalakar


> No virus found in this incoming message.
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  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
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<body bgcolor="#ffffff" text="#000000">
Hi Iain<br>
We have developed a new method called GQSAR method. It explains the
reason for making particular&nbsp; chemical substitutions or&nbsp; also suggest
with simplistic way..GQSAR provides researchers with very important
site-specific clues for better lead design and also for lead hopping.<br>
For more information Please visit <a class="moz-txt-link-abbreviated" href="http://www.VLifeSciences.com">www.VLifeSciences.com</a><br>
<br>
<div class="moz-signature">
<meta http-equiv="Content-Type" content="text/html; ">
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<p class="style1">Best Regards,<br>
Kamalakar</p>
<br>
</div>
<blockquote
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