From owner-chemistry@ccl.net Fri Mar 7 03:37:00 2008
From: "ALBERT POATER TEIXIDOR albert.poater%a%udg.edu" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: KIE calculations
Message-Id: <-36446-080307024027-7475-hfN7HZ/8nwubscc8pMREtA**server.ccl.net>
X-Original-From: "ALBERT POATER TEIXIDOR" <albert.poater!A!udg.edu>
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Date: Fri, 7 Mar 2008 08:26:01 +0100 (CET)
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Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater[#]udg.edu]
Thanks for the answer about KIE. I failed in writing the question I think.
I wanted to know how it is prepared an input of Gaussian when changing the
mass of hydrogen (=1) to deuterium (=2). The manual talks about keywords
like readisotopes, but it is not clear for me how to prepare it.
Thanks again,
Albert
>
> Sent to CCL by: "Alexander Hoepker" [achoepker=-=gmail.com]
> Dear Albert,
> this will require you to calculate ground state and transition
> energies of the protio and deuterio forms (assuming this is the
> isotopic substitution you're referring to). The KIE can then be
> computed by taking the exponential of the difference in the activation
> free energies according to the Eyring equation
> (k1/k2=exp(deltaG2-deltaG1) where deltaG is the difference of ground
> state and transition state energies.
>
> Hope this helps
> Alex
>
> On Thu, Mar 6, 2008 at 3:05 PM, ALBERT POATER TEIXIDOR
> albert.poater{=}udg.edu <owner-chemistry|ccl.net> wrote:
>>
>> Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater[-]udg.edu]
>> Dear CCL members,
>> Could you explain me the easiest way to calculate the KIE from Guassian
>> optimizations in order to compare the KIE of two different patways?
>> Thanks in advance,
>> Albert>
>
>
From owner-chemistry@ccl.net Fri Mar 7 05:24:00 2008
From: "Ulrich Scharfenort scharfenort a ltt.rwth-aachen.de" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL:G: g03 Problem with "HinderedRotor" calculations
Message-Id: <-36447-080307052304-17735-8+4vcRJZBkwaSgsIpMiJ2Q/a\server.ccl.net>
X-Original-From: Ulrich Scharfenort <scharfenort]-[ltt.rwth-aachen.de>
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Date: Fri, 07 Mar 2008 11:22:51 +0100
MIME-version: 1.0
Sent to CCL by: Ulrich Scharfenort [scharfenort=ltt.rwth-aachen.de]
Hello,
I hope maybe one of you can help me with an problem.
Currently i try to calculate Aromatic compounds with the HinderedRotor
option. With Alkanes HR works very fine and without any problem so I
think it's not an problem with the coordinates.
The error-message is as follows:
Number of internal rotation degrees of freedom = 4
NNew= 30 NTest= 4 NB= 10 IFrz= 0 IBar= 0 ICyc= 0
Problem with the number of degrees of freedom
Error termination via Lnk1e in
/opt/GAUSSIAN/LINUX_amd64/g03.d02/l716.exe at Fri Mar 7 11:10:19 2008.
Job cpu time: 0 days 0 hours 0 minutes 15.4 seconds.
File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 10
Scr= 1
This was a calculation for Butylbenzene where are internal rotations.
Does HR only work for Alkanes and nothing else?
Maybe somebody does know for which compound classes HR works and for
which not or and way to make it working for all compounds.
I will appreciate all the help you can provide on this problem.
Yours sincerely
<http://dict.leo.org/ende?lp=ende&p=eL4jU.&search=Yours>
Ulrich Scharfenort
From owner-chemistry@ccl.net Fri Mar 7 05:58:00 2008
From: "Andreas Bick andreas.bick!A!scienomics.com" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: VASP:how to calculate phonon spectrum ?
Message-Id: <-36448-080307052026-17473-uA6x8AHIyhTggIoGkQQnkA,,server.ccl.net>
X-Original-From: Andreas Bick <andreas.bick .. scienomics.com>
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Date: Fri, 07 Mar 2008 10:38:22 +0100
MIME-Version: 1.0
Sent to CCL by: Andreas Bick [andreas.bick[a]scienomics.com]
Dear Guanna,
if you are looking for open source code to do this kind of calculations
you might want to take a look at ABINIT:
http://www.abinit.org/
Regards
Andreas
>Sent to CCL by: "Guanna Li" [gnli*dicp.ac.cn]
>
>Dear CCLer,
>dose anybody have some experience in calculating phonon spectrum by VASP?
>could anybody please give me an example of the input file or recommend another opensource process ?
>Thanks in advance!
>
>--------------
>2008-03-07
>Best wishes
>Guanna Li
>Email: gnli]^[dicp.ac.cn>
>
>
>
>
--
Dr. Andreas Bick
Scienomics SARL
Sales and Marketing
mobile: +491621309945
From owner-chemistry@ccl.net Fri Mar 7 06:34:01 2008
From: "Rene Thomsen rt(0)molegro.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: Molegro releases Molegro Data Modeller v1.1.0
Message-Id: <-36449-080307051929-17351-SgOtoplVBBcb3k/rwMjEJg-x-server.ccl.net>
X-Original-From: "Rene Thomsen" <rt(0)molegro.com>
Date: Fri, 7 Mar 2008 05:19:22 -0500
Sent to CCL by: "Rene Thomsen" [rt{:}molegro.com]
Aarhus, Denmark, March 7th, 2008 - Molegro is pleased to announce a new release of Molegro Data Modeller, a cross-platform application for Data Mining, Data Modelling, and Data Visualization.
Molegro Data Modeller offers a high-quality modelling tool based on state-of-the-art data mining techniques combined with a user interface experience focusing on usability and productivity.
Molegro Data Modeller utilizes a spreadsheet centered user interface making it a simple and affordable alternative to complex workflow based solutions or command-driven statistical products. Molegro Data Modeller runs on Windows, Linux, and Mac OS X.
New features in version 1.1:
* Partial Least Squares regression.
* Similarity Browser for quick inspection of similar data points using several similarity measures.
* Linear kernel for SVM regression.
* Conversion between numerical and textual columns (and vice versa).
* Miscellaneous bug fixes (see the Release Notes for details).
For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact:
Rene Thomsen, CEO
Molegro
Hoegh-Guldbergs Gade 10, Bldg. 1090
DK-8000 Aarhus
Denmark
E-mail: rt() molegro.com
Phone: (+45) 89 42 31 65
About Molegro
Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience.
From owner-chemistry@ccl.net Fri Mar 7 07:09:01 2008
From: "Senthilnathan Dhurairajan zenthil03^-^yahoo.co.in" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: modredundant key usage problem
Message-Id: <-36450-080307064949-10678-jcfEe75lMJupChHKFMjiSQ[*]server.ccl.net>
X-Original-From: "Senthilnathan Dhurairajan" <zenthil03]|[yahoo.co.in>
Date: Fri, 7 Mar 2008 06:49:44 -0500
Sent to CCL by: "Senthilnathan Dhurairajan" [zenthil03]~[yahoo.co.in]
Dear CCL'rs
I have used modredundant key for atom freezing purpose in my enzyme transition state modeling calculation at the level of AM1. I have error repeatedly at the link of L9999 (finalising output). How can I avoid this error. Please give your sugessions.
thanking you in advance
Senbthilnathan
From owner-chemistry@ccl.net Fri Mar 7 09:22:00 2008
From: "George B Pal pal[a]physik.uni-kl.de" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: gamess coulomb integrals
Message-Id: <-36451-080307044454-12424-rFu2R4IyGHa40ZIPBNn9dw_+_server.ccl.net>
X-Original-From: "George B Pal" <pal=physik.uni-kl.de>
Date: Fri, 7 Mar 2008 04:44:49 -0500
Sent to CCL by: "George B Pal" [pal a physik.uni-kl.de]
Hi all,
how can I extract the Coulomb integrals (i.e. the electron repulsion integrals matrix elements <n1n2|n3n4>, n1,n2,n3,n4=MOs) from a gamess HF calculation?
Also, how are the ERI stored?
Thanks a lot
George Pal
TU Kaiserslatern Germany
From owner-chemistry@ccl.net Fri Mar 7 09:57:01 2008
From: "Jean-Christophe Poully poully:+:galilee.univ-paris13.fr" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: Problem with Oniom charge embedding option
Message-Id: <-36452-080307053950-25954-Ub3JzeBAgFsxQFm5Y56opA##server.ccl.net>
X-Original-From: "Jean-Christophe Poully" <poully^^^galilee.univ-paris13.fr>
Date: Fri, 7 Mar 2008 05:39:46 -0500
Sent to CCL by: "Jean-Christophe Poully" [poully%galilee.univ-paris13.fr]
Hello!
I am trying to optimize the structure of a 12-amino acid peptide with Oniom at the B3LYP/6-31g(d):AM1 level, and I would like to allow the wavefunction to be polarized by electronic embedding because a NH3+ group belongs to the AM1 part of the calculation. I tried many things with the input file, like typing "# opt freq oniom(b3lyp/6-31g(d):am1) embedcharge " or "# opt freq oniom(b3lyp/6-31g(d):am1=embedcharge) ", but without any success... Recently, I have found a test job called "test554.gjf" which is:
#p oniom=(hf/3-21g:amber)=scale=3 test opt freq
Gaussian Test Job 554:
ONIOM with charge embedding
0 1 -1 1
C-CT--0.249300 0 2.249208 4.416226 -0.000000 H
C-C-0.723100 0 1.776359 5.862911 -0.000000 H
H-H1-0.105600 0 2.853770 4.240670 0.889823 H
H-H1-0.105600 0 2.853770 4.240670 -0.889823 H
O-O2--0.785500 0 0.576029 6.126821 -0.000000 H
O-O2--0.785500 0 2.589112 6.784796 0.000000 H
N-N--0.382100 0 1.115208 3.514202 0.000000 L H-H1-0.105600
N-N3-0.294300 0 0.571973 -0.133569 0.000000 L
H-H-0.164200 0 -0.243057 -0.730081 -0.000000 L
C-CT--0.010000 0 0.121803 1.243728 0.000000 L
H-H-0.164200 0 1.062396 -0.254028 0.874686 L
H-H-0.164200 0 1.062396 -0.254028 -0.874686 L
C-C-0.616300 0 1.312933 2.191196 0.000000 L
H-HP-0.089500 0 -0.479554 1.429966 -0.889823 L
H-HP-0.089500 0 -0.479554 1.429966 0.889823 L
O-O--0.572200 0 2.483771 1.729991 0.000000 L
H-H-0.268100 0 0.184791 3.880704 -0.000000 L
Therefore I have tried to type "# opt freq oniom(b3lyp/6-31g(d):am1)=scale=3 " and it seems to work, at least it is running, but can somebody tell me what Gaussian is actually doing and what does "=scale=3" means? I would be extremely grateful...
Thank you very much!
Jean-Christophe Poully
PhD student at the Paris 13 University
poully-,-galilee.univ-paris13.fr
From owner-chemistry@ccl.net Fri Mar 7 10:32:01 2008
From: "Kalpana Krishnaswami kalpuk*_*gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: calculating and displaying surface residues
Message-Id: <-36453-080307025827-8839-JbmysGzLgSMkXNqIi9yUSQ,server.ccl.net>
X-Original-From: "Kalpana Krishnaswami" <kalpuk^_^gmail.com>
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boundary="----=_Part_3595_19233832.1204861864481"
Date: Fri, 7 Mar 2008 09:21:04 +0530
MIME-Version: 1.0
Sent to CCL by: "Kalpana Krishnaswami" [kalpuk%a%gmail.com]
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Hi
We would like to calculate and display exposed hydrophobic surfaces on a
protein. We would also like to list the residues on the surface. Are there
freeware/ scripts/plugins to pymol/rasmol that would do this?
Thanks
--
Kalpana Krishnaswami
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<br clear="all">Hi<br>We would like to calculate and display exposed hydrophobic surfaces on a protein. We would also like to list the residues on the surface. Are there freeware/ scripts/plugins to pymol/rasmol that would do this?<br>
Thanks<br>-- <br>Kalpana Krishnaswami
------=_Part_3595_19233832.1204861864481--
From owner-chemistry@ccl.net Fri Mar 7 11:06:00 2008
From: "Alcides Simao alsimao(~)gmail.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: modredundant key usage problem
Message-Id: <-36454-080307092738-22745-Vd4FZmAF9v3BJ6giGEpnSg**server.ccl.net>
X-Original-From: "Alcides Simao" <alsimao-$-gmail.com>
Content-Type: multipart/alternative;
boundary="----=_Part_5098_3094350.1204900046405"
Date: Fri, 7 Mar 2008 14:27:26 +0000
MIME-Version: 1.0
Sent to CCL by: "Alcides Simao" [alsimao|gmail.com]
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Dear Senthilnathan
I hope that this link helps you.
http://www.gaussian.com/g_gv/gv3/modred.htm
You can only freeze atoms by making use of cartesian coordinates.
Remember that, in z-matrix, you can only freeze bonds, angles and dihedrals!
In matter of fact, z-matrix only has one coordinate defined by one atom :
the first line, from which all other atoms are described.
But I am not completely sure of this! My experience is rather limited!
Best Regards,
Alcides
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Dear Senthilnathan <br><br>I hope that this link helps you.<br><br><a href="http://www.gaussian.com/g_gv/gv3/modred.htm">http://www.gaussian.com/g_gv/gv3/modred.htm</a><br><br>You can only freeze atoms by making use of cartesian coordinates.<br>
Remember that, in z-matrix, you can only freeze bonds, angles and dihedrals!<br>In matter of fact, z-matrix only has one coordinate defined by one atom : the first line, from which all other atoms are described.<br><br>But I am not completely sure of this! My experience is rather limited!<br>
<br>Best Regards,<br><br>Alcides<br>
------=_Part_5098_3094350.1204900046405--
From owner-chemistry@ccl.net Fri Mar 7 11:41:00 2008
From: "Erdem YILDIRIM ekyildirim-$-gmail.com" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL:G: KIE calculations
Message-Id: <-36455-080307085529-17821-AhQ092k8fVcoKMEhYbtBzA-.-server.ccl.net>
X-Original-From: "Erdem YILDIRIM" <ekyildirim*|*gmail.com>
Content-Language: tr
Content-Transfer-Encoding: quoted-printable
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charset="utf-8"
Date: Fri, 7 Mar 2008 14:11:08 +0200
MIME-Version: 1.0
Sent to CCL by: "Erdem YILDIRIM" [ekyildirim*gmail.com]
Hi=20
Please try to arrange your coordinates in the .com file according to the =
example below
cs(Iso=3D135) 0.929569000 0.325900000 -0.555581000
8 4.051779000 0.684676000 -1.673610000
1 4.045778000 1.626992000 -1.991730000
That should work.=20
Erdem
-----Original Message-----
> From: owner-chemistry ~ ccl.net [mailto:owner-chemistry ~ ccl.net]=20
Sent: Friday, March 07, 2008 9:26 AM
To: YILDIRIM, Erdem
Subject: CCL:G: KIE calculations
Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater[#]udg.edu]
Thanks for the answer about KIE. I failed in writing the question I =
think.
I wanted to know how it is prepared an input of Gaussian when changing =
the
mass of hydrogen (=3D1) to deuterium (=3D2). The manual talks about =
keywords
like readisotopes, but it is not clear for me how to prepare it.
Thanks again,
Albert
>
> Sent to CCL by: "Alexander Hoepker" [achoepker=3D-=3Dgmail.com]
> Dear Albert,
> this will require you to calculate ground state and transition
> energies of the protio and deuterio forms (assuming this is the
> isotopic substitution you're referring to). The KIE can then be
> computed by taking the exponential of the difference in the activation
> free energies according to the Eyring equation
> (k1/k2=3Dexp(deltaG2-deltaG1) where deltaG is the difference of ground
> state and transition state energies.
>
> Hope this helps
> Alex
>
> On Thu, Mar 6, 2008 at 3:05 PM, ALBERT POATER TEIXIDOR
> albert.poater{=3D}udg.edu <owner-chemistry|ccl.net> wrote:
>>
>> Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater[-]udg.edu]
>> Dear CCL members,
>> Could you explain me the easiest way to calculate the KIE from =
Guassian
>> optimizations in order to compare the KIE of two different patways?
>> Thanks in advance,
>> Albert>
>
>
-=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=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =
search)http://www.ccl.net/spammers.txt
From owner-chemistry@ccl.net Fri Mar 7 12:16:00 2008
From: "Alexander Hoepker achoepker() gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: KIE calculations
Message-Id: <-36456-080307085548-17873-xvv5JyBnFTLHgcCe4VRfCQ]_[server.ccl.net>
X-Original-From: "Alexander Hoepker" <achoepker^gmail.com>
Content-Disposition: inline
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Date: Fri, 7 Mar 2008 08:55:32 -0500
MIME-Version: 1.0
Sent to CCL by: "Alexander Hoepker" [achoepker^gmail.com]
Albert,
When computing the protio ground- and transition states, be sure to
indicate to save it as a checkpoint file (%Chk=3D'name'). Then load this
checkpoint file with the following input when computing the deutero
form:
%Chk=3D'name' (checkpoint file that was saved earlier)
#T B3LYP/6-31G(d) Geom=3DCheckpoint Freq=3D(ReadIsotopes) Test
0, 1
12 (atomic masses of atoms, this is where isotopes are specified)
1
1
1
7
=85
On Fri, Mar 7, 2008 at 2:26 AM, ALBERT POATER TEIXIDOR
albert.poater%a%udg.edu <owner-chemistry(~)ccl.net> wrote:
>
> Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater[#]udg.edu]
> Thanks for the answer about KIE. I failed in writing the question I thin=
k.
> I wanted to know how it is prepared an input of Gaussian when changing t=
he
> mass of hydrogen (=3D1) to deuterium (=3D2). The manual talks about keyw=
ords
> like readisotopes, but it is not clear for me how to prepare it.
> Thanks again,
> Albert
>
>
> >
> > Sent to CCL by: "Alexander Hoepker" [achoepker=3D-=3Dgmail.com]
> > Dear Albert,
> > this will require you to calculate ground state and transition
> > energies of the protio and deuterio forms (assuming this is the
> > isotopic substitution you're referring to). The KIE can then be
> > computed by taking the exponential of the difference in the activation
> > free energies according to the Eyring equation
> > (k1/k2=3Dexp(deltaG2-deltaG1) where deltaG is the difference of ground
> > state and transition state energies.
> >
> > Hope this helps
> > Alex
> >
> > On Thu, Mar 6, 2008 at 3:05 PM, ALBERT POATER TEIXIDOR
> > albert.poater{=3D}udg.edu <owner-chemistry|ccl.net> wrote:
> >>
> >> Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater[-]udg.edu]
> >> Dear CCL members,
> >> Could you explain me the easiest way to calculate the KIE from Guass=
ian
> >> optimizations in order to compare the KIE of two different patways?
> >> Thanks in advance,
> >> Albert>
> >
> >
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: search=
)>
>
>
From owner-chemistry@ccl.net Fri Mar 7 12:51:01 2008
From: "sherin falah shireenfalah(0)hotmail.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: gamess error message ($DET keyword)
Message-Id: <-36457-080307115909-18729-eJX8e3k/uaMacvxBZLCB/g . server.ccl.net>
X-Original-From: "sherin falah" <shireenfalah~!~hotmail.com>
Date: Fri, 7 Mar 2008 11:59:05 -0500
Sent to CCL by: "sherin falah" [shireenfalah^_^hotmail.com]
Dear CCL users,
I am trying to submit some calculations using gamess us but my jobs crashed always.
My input files looks like:
$CONTRL SCFTYP=MCSCF MULT=1 RUNTYP=ENERGY $END
$FORCE METHOD=ANALYTIC $END
$MCSCF CISTEP=ALDET MAXIT=480 FULLNR=.T. $END
$DET GROUP=1 NCORE=18 NACT=6 NELS=6 ISTSYM=1 NSTATE=4 SZ=0 WSTATE(1)=1,1,0,0 $END
$STATPT NSTEP=120 $END
The error message I got is :
INCORRECT DATA VALUE FOUND
**** ERROR READING INPUT GROUP $DET *****
THE PROBLEM IS WITH THIS INPUT LINE, NEAR THE X MARKER
$STATPT NSTEP=120 $END
X
I am sure that the error is not in the "STATPT" keyword because I got similar message whatever keywords I put in the line after the $DET line.
I tried to rewrite the file again to come over any hidden format problem but this did not help. I have no clue what is going wrong here.
Any help would be really appreciated.
Thanks in advance.
Best regards,
Shireen Falah
From owner-chemistry@ccl.net Fri Mar 7 14:36:00 2008
From: "Elaine Meng meng()cgl.ucsf.edu" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: calculating and displaying surface residues
Message-Id: <-36458-080307132355-23297-Umg5wU1zJc42GSdLUaLaFw]![server.ccl.net>
X-Original-From: "Elaine Meng" <meng{}cgl.ucsf.edu>
Date: Fri, 7 Mar 2008 13:23:52 -0500
Sent to CCL by: "Elaine Meng" [meng]=[cgl.ucsf.edu]
On Mar 6, 2008, at 7:51 PM, Kalpana Krishnaswami kalpuk*_*gmail.com wrote:
Hi
We would like to calculate and display exposed hydrophobic surfaces on a protein. We would also like to list the residues on the surface. Are there freeware/ scripts/plugins to pymol/rasmol that would do this?
Thanks
--
Kalpana Krishnaswami
Hi Kalpana,
If you want calculations based on the hydrophobicity of each atom, take a look at the GetArea server:
http://pauli.utmb.edu/cgi-bin/get_a_form.tcl
If you want calculations based on the hydrophobicity of amino acid residues in proteins, you may want to try UCSF Chimera - not a web server, but freely downloadable for noncommercial use (Windows, Mac, Linux, etc.):
http://www.cgl.ucsf.edu/chimera/index.html
I recommend the recent snapshot:
http://www.cgl.ucsf.edu/chimera/download.html#snapshots
In Chimera, there are many related possibilities. After opening the structure ("File... Open" for local file or "File... Fetch by ID" to get from PDB) you could
(A) color the surface by amino acid hydrophobicity - simply choosing "Presets... interactive 3 (hydrophobicity surface)" from the menu will apply a built-in scheme. Or to specify the color mapping yourself, use the "Render by Attribute" tool (under Tools... Depiction) on the residue attribute named kdHydrophobicity.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html
(B) calculate surface area values - first calculate the surface areas for all atoms, then later you can sum over subsets such as the hydrophobic residues. To calculate atomic surface areas, use the "Area/Volume from Web" tool (under Tools... Surface/Binding Analysis) and pick which surface area method and parameters you want.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html
After that, to sum over only residues with a certain hydrophobicity, first select them with "Select... by Attribute Value" and then with "Attribute Calculator" (under Tools... Structure Analysis), sum the surface area values of all selected atoms in the whole model. Similarly, to get a list of all surface residues, you could select all atoms with surface area >0 and then use "Actions... Write List" to make a text file listing those residues or "Actions... Write PDB" to save the coordinates of those residues.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html
The Kyte-Doolittle amino acid hydrophobicity is used by default, but you can use different scales.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html
I realize there is a learning curve with Chimera, but you can do many powerful things. I can provide more details if you try any of these things but get stuck.
Best,
Elaine
-----
Elaine C. Meng, Ph.D. meng###cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
From owner-chemistry@ccl.net Fri Mar 7 15:10:00 2008
From: "rossi^-^york.cuny.edu" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: gamess error message ($DET keyword)
Message-Id: <-36459-080307143640-12290-ttOefHZc2ksTmgkYlb+H5w[]server.ccl.net>
X-Original-From: rossi*_*york.cuny.edu
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset=ISO-8859-1;
format="flowed"
Date: Fri, 07 Mar 2008 13:45:22 -0500
MIME-Version: 1.0
Sent to CCL by: rossi(0)york.cuny.edu
Hello:
The line
> $DET GROUP=1 NCORE=18 NACT=6 NELS=6 ISTSYM=1 NSTATE=4 SZ=0
> WSTATE(1)=1,1,0,0 $END
is probably too long and getting truncated.
Try this instead:
$DET GROUP=1 NCORE=18 NACT=6 NELS=6 ISTSYM=1
NSTATE=4 SZ=0 WSTATE(1)=1,1,0,0 $END
Regards,
A. R. Rossi