From owner-chemistry@ccl.net Mon Jan 31 09:15:01 2011 From: "Jean Jules FIFEN julesfifen_-_gmail.com" To: CCL Subject: CCL: Polyrate 2010 atoms limitation Message-Id: <-43802-110131090209-31630-xBcofD9mlksDMLX78CYRxQ-#-server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=00163628412e25cffd049b24dbc0 Date: Mon, 31 Jan 2011 15:01:44 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen()gmail.com] --00163628412e25cffd049b24dbc0 Content-Type: text/plain; charset=ISO-8859-1 Dear all, Please, does everyone know if Polyrate 2010 software is always limited to 10-atoms systems as its previous versions? Thanks a lot in advance. -- Jean Jules FIFEN. University of Douala, Cameroon Faculty of Science Laboratoire de Physique Fondamentale --00163628412e25cffd049b24dbc0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all,
Please, does everyone know if Polyrate 2010 s= oftware is always limited to 10-atoms systems as its previous versions?
=
Thanks a lot in advance.

--
<= font size=3D"4">Jean Jules FIFEN.=
University of Douala, Cameroon
Faculty of Science
Laboratoire de Phys= ique Fondamentale

--00163628412e25cffd049b24dbc0-- From owner-chemistry@ccl.net Mon Jan 31 10:06:00 2011 From: "WATOC watoc2011|-|uam.es" To: CCL Subject: CCL: WATOC 2011 - Reminder Message-Id: <-43803-110131071430-27800-Sn8pi/0nunbLS8NzEJnLuQ-*-server.ccl.net> X-Original-From: "WATOC " Date: Mon, 31 Jan 2011 07:14:27 -0500 Sent to CCL by: "WATOC " [watoc2011^uam.es] Dear Colleagues, We would like to remind you that the deadline for submitting abstracts to WATOC-2011 is March, 1. The deadline for early registration is April, 1. There will be about 90 slots for oral presentations. In case you wish to apply for an oral presentation (8 +2 min.) please click in the corresponding option, when you submit your abstract (www.watoc2011.com) We also remind you that there will be prizes for the best posters presented to the Conference. Do not lose the opportunity to participate in the major worldwide event that brings together an international network of theoretical and computational chemists. Please remember that Santiago attracts a lot of visitors at this time of the year, so it is advisable to have your accommodation booked as soon as possible. If you have already registered and submitted your abstract please discard this message. We are looking forward to seeing you in Santiago next July. Best regards Manuel and Otilia, Chairpersons From owner-chemistry@ccl.net Mon Jan 31 10:40:00 2011 From: "Henry Martinez hmartine~~gmail.com" To: CCL Subject: CCL: Restart Freq calculation Message-Id: <-43804-110131103021-607-EEHYao/OGjctcXuO9i3fkQ]=[server.ccl.net> X-Original-From: "Henry Martinez" Date: Mon, 31 Jan 2011 10:30:19 -0500 Sent to CCL by: "Henry Martinez" [hmartine:_:gmail.com] Hello everyone, This is the first time I need to restart a Freq calculation (I need some thermochemistry data) and I am using this input ONLY %chk=n9.chk %nproc=2 %mem=120MW # freq=Restart b3lyp/6-311+g(3df,2p) However the calculation started and finished in "Normal termination" in less than 20 sec, without any Thermochemistry data, obviously that is not what I want. Can anybody tell what am I doing wrong and how can I fixed. Thanks you very much for your help. From owner-chemistry@ccl.net Mon Jan 31 11:15:01 2011 From: "Jean Jules FIFEN julesfifen|-|gmail.com" To: CCL Subject: CCL: Maximum Force and RMS force not coverged. What should I do? Message-Id: <-43805-110131064741-16963-Bx7LHZKrYplRh97PuYnusA+/-server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=0015175cd630694e74049b22f9ef Date: Mon, 31 Jan 2011 12:47:02 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen_+_gmail.com] --0015175cd630694e74049b22f9ef Content-Type: text/plain; charset=ISO-8859-1 Dear Ehsan, Try restarting your job from the last point by calculating analytic hessian at the first step. So modify the key word opt onto opt=calcfc. You can also add the key word nosymm if you don't need a constraint symmetry. Hope this will help, Best regards, On 30 January 2011 12:09, Ehsan shakerzadeh ehsan_shakerzadeh() yahoo.com < owner-chemistry[A]ccl.net> wrote: > > Sent to CCL by: "Ehsan shakerzadeh" [ehsan_shakerzadeh|*|yahoo.com] > Dear All, > I run a job for a week. after a week Maximum Displacement and RMS > Displacement are converged but Maximum Force and RMS force are not > converged.some last SCF steps are also appered: > SCF Done: E(RB+HF-LYP) = -3193.08688985 A.U. after 17 cycles > SCF Done: E(RB+HF-LYP) = -3193.09622481 A.U. after 12 cycles > SCF Done: E(RB+HF-LYP) = -3193.09657987 A.U. after 16 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662031 A.U. after 9 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662458 A.U. after 8 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662526 A.U. after 6 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662536 A.U. after 4 cycles > SCF Done: E(RB+HF-LYP) = -3193.08688985 A.U. after 17 cycles > SCF Done: E(RB+HF-LYP) = -3193.09622481 A.U. after 12 cycles > SCF Done: E(RB+HF-LYP) = -3193.09657987 A.U. after 16 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662031 A.U. after 9 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662458 A.U. after 8 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662526 A.U. after 6 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662536 A.U. after 6 cycles > SCF Done: E(RB+HF-LYP) = -3193.08688994 A.U. after 17 cycles > SCF Done: E(RB+HF-LYP) = -3193.09622477 A.U. after 12 cycles > SCF Done: E(RB+HF-LYP) = -3193.09657986 A.U. after 16 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662030 A.U. after 9 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662457 A.U. after 8 cycles > SCF Done: E(RB+HF-LYP) = -3193.09662526 A.U. after 6 cycles > > SCF is converged but again go to first step. > I would be pleased if anyone can help me to remove this problem. > Thanks in advance. > Ehsan> > > -- Jean Jules FIFEN. --0015175cd630694e74049b22f9ef Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Ehsan,
Try restarting your job from the last point= by calculating analytic hessian at the first step. So modify the key word = opt onto opt=3Dcalcfc. You can also add the key word nosymm if you don'= t need a constraint symmetry.
Hope this will help,

Best regards,

On 30 January 2011 12:09, Ehsan shakerzadeh ehsan_shakerzadeh() yahoo.com <owner-chemistry[A]ccl.net> wrote:

Sent to CCL by: "Ehsan =A0shakerzadeh" [ehsan_shakerzadeh|*|yahoo.com]
Dear All,
I run a job for a week. after a week =A0Maximum Displacement and RMS =A0 = =A0 Displacement are converged but Maximum Force and =A0RMS force are not c= onverged.some last SCF steps are also appered:
SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.08688985 =A0 =A0 A.U. after =A0 17 c= ycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09622481 =A0 =A0 A.U. after =A0 1= 2 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09657987 =A0 =A0 A.U. after =A0 1= 6 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662031 =A0 =A0 A.U. after =A0 = =A09 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662458 =A0 =A0 A.U. after =A0 = =A08 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662526 =A0 =A0 A.U. after =A0 = =A06 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662536 =A0 =A0 A.U. after =A0 = =A04 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.08688985 =A0 =A0 A.U. after =A0 1= 7 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09622481 =A0 =A0 A.U. after =A0 1= 2 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09657987 =A0 =A0 A.U. after =A0 1= 6 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662031 =A0 =A0 A.U. after =A0 = =A09 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662458 =A0 =A0 A.U. after =A0 = =A08 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662526 =A0 =A0 A.U. after =A0 = =A06 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662536 =A0 =A0 A.U. after =A0 = =A06 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.08688994 =A0 =A0 A.U. after =A0 1= 7 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09622477 =A0 =A0 A.U. after =A0 1= 2 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09657986 =A0 =A0 A.U. after =A0 1= 6 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662030 =A0 =A0 A.U. after =A0 = =A09 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662457 =A0 =A0 A.U. after =A0 = =A08 cycles
=A0SCF Done: =A0E(RB+HF-LYP) =3D =A0-3193.09662526 =A0 =A0 A.U. after =A0 = =A06 cycles

SCF is converged but again go to first step.
I would be pleased if anyone can help me to remove this problem.
Thanks in advance.
Ehsan



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--
Jean Jules FIFEN.

--0015175cd630694e74049b22f9ef-- From owner-chemistry@ccl.net Mon Jan 31 11:58:00 2011 From: "Jean Jules FIFEN julesfifen^-^gmail.com" To: CCL Subject: CCL:G: Restart Freq calculation Message-Id: <-43806-110131115551-4493-K7V8DzUnn8FquCzm0p7Iwg^^server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=000e0cd3aa9aca7402049b274835 Date: Mon, 31 Jan 2011 17:55:34 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen[*]gmail.com] --000e0cd3aa9aca7402049b274835 Content-Type: text/plain; charset=ISO-8859-1 Dear Martinez, It is worth mentioning that with gaussian versions, you can restart a lot of jobs, but unfortunately, you can not do likewise concerning frequency calculation. So you have to do the frequency calculation again. It is easy as your are already saved the checkpoint file. Just do: # freq b3lyp/6-311+g(3df,2p) guess=read geom=allcheck test Hope this would help. Best Reagrds, On 31 January 2011 16:30, Henry Martinez hmartine~~gmail.com < owner-chemistry . ccl.net> wrote: > > Sent to CCL by: "Henry Martinez" [hmartine:_:gmail.com] > Hello everyone, > This is the first time I need to restart a Freq calculation (I need some > thermochemistry data) and I am using this input ONLY > > %chk=n9.chk > %nproc=2 > %mem=120MW > # freq=Restart b3lyp/6-311+g(3df,2p) > > However the calculation started and finished in "Normal termination" in > less than 20 sec, without any Thermochemistry data, obviously that is not > what I want. Can anybody tell what am I doing wrong and how can I fixed. > Thanks you very much for your help.> > > -- Jean Jules FIFEN. UNIVERSITY OF DOUALA, Cameroon Faculty of Science Laboratoire de Physique Fondamentale --000e0cd3aa9aca7402049b274835 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Martinez,
It is worth mentioning that with gaussia= n versions, you can restart a lot of jobs, but unfortunately, you can not d= o likewise concerning frequency calculation. So you have to do the frequenc= y calculation again. It is easy as your are already saved the checkpoint fi= le. Just do: # freq b3lyp/6-311+g(3df,2p) guess=3Dread geom=3Dallcheck test=

Hope this would help.

Best Reagrds,

On 31 January 2011 16:30, Henry Martinez hmartine~~gmail.com <owner-chemistry . ccl.net> wrote:

Sent to CCL by: "Henry =A0Martinez" [hmartine:_:gmail.com]
Hello everyone,
This is the first time I need to restart a Freq calculation (I need some th= ermochemistry data) and I am using this input ONLY

%chk=3Dn9.chk
%nproc=3D2
%mem=3D120MW
# freq=3DRestart b3lyp/6-311+g(3df,2p)

However the calculation started and finished in "Normal termination&qu= ot; in less than 20 sec, without any Thermochemistry data, obviously that i= s not what I want. Can anybody tell what am I doing wrong and how can I fix= ed. Thanks you very much for your help.



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Jean Jules FIFEN.
U= NIVERSITY OF DOUALA, Cameroon
Faculty of Science
Laboratoire de Physi= que Fondamentale

--000e0cd3aa9aca7402049b274835-- From owner-chemistry@ccl.net Mon Jan 31 12:37:00 2011 From: "Jamin Krinsky krinsky.jamin-,-gmail.com" To: CCL Subject: CCL:G: Restart Freq calculation Message-Id: <-43807-110131123534-697-tvgWYgaXviiiv2ZuBR7q7g[a]server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 31 Jan 2011 09:35:15 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin[*]gmail.com] Hi Henry, In G03 (and I'm pretty sure G09 also) analytical frequency calculations cannot be restarted. If you can do that in G09, then you'd probably need the rwf file from the previous run, which you probably don't have. If you often run frequency calculations that might need restarting you can do them numerically (freq=numer I think) but that will generally take a lot longer. Jamin On Mon, Jan 31, 2011 at 7:30 AM, Henry Martinez hmartine~~gmail.com wrote: > > Sent to CCL by: "Henry  Martinez" [hmartine:_:gmail.com] > Hello everyone, > This is the first time I need to restart a Freq calculation (I need some thermochemistry data) and I am using this input ONLY > > %chk=n9.chk > %nproc=2 > %mem=120MW > # freq=Restart b3lyp/6-311+g(3df,2p) > > However the calculation started and finished in "Normal termination" in less than 20 sec, without any Thermochemistry data, obviously that is not what I want. Can anybody tell what am I doing wrong and how can I fixed. Thanks you very much for your help.>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Mon Jan 31 13:12:00 2011 From: "Mihaly Mezei Mihaly.Mezei,+,mssm.edu" To: CCL Subject: CCL: Calculating surface hydrophobicity Message-Id: <-43808-110131130342-11885-wOqHRelrpQaR0etPX1ZVlg^server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Mon, 31 Jan 2011 13:03:14 -0500 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei:_:mssm.edu] > I want to calculate the surface hydrophobicity of a protein molecule, but so > far I only manage to use atomic partial charges as the estimate of > the surface hydrophobicity, anyone can provide me some insight on how well is > that as an estimate..? There are a number of residue-based hydrophobicity/hydropathy scales. Good resources (references, values) for such scales are the paper J. Cornette, K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky and C. DeLisi, Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic Structures in Proteins, J. Mol. Biol., 195, 659-685 (1987). > Also, it will be great help if anyone knows of any software/webtools/ that > calculates surface hyrdrophobicity of protein, which generates some > kind of grid output file. My program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can get the hydrophobicity (hydropathy) values of the residue the atom belongs to and put into the temperature factor column (the user can choose among Kyte-Doolittle, Eisenberg or White's scale or input a new one) - so you can visualize it easily in your favorite molecule viewer. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Mon Jan 31 13:46:00 2011 From: "RD Miles rdmsgl^^^gmail.com" To: CCL Subject: CCL: Theory Message-Id: <-43809-110131131851-25838-TSV2hu6xlMayg7/XHIT1vQ],[server.ccl.net> X-Original-From: RD Miles Content-Type: multipart/alternative; boundary=0015175cb4ac8deb9d049b28718d Date: Mon, 31 Jan 2011 13:18:01 -0500 MIME-Version: 1.0 Sent to CCL by: RD Miles [rdmsgl=gmail.com] --0015175cb4ac8deb9d049b28718d Content-Type: text/plain; charset=ISO-8859-1 Sorry for the reply to an old thread, but I thought I would mention that Szabo and Ostlund do address CC in chapter 5. On Wed, Jan 12, 2011 at 3:06 AM, Johannes Johansson johjo76(-)gmail.com < owner-chemistry(_)ccl.net> wrote: > for the basic theory (Hartree-Fock, Moller-Plesset perturbation theory, CI > etc) I know few books that are as detailed as "Modern Quantum Chemistry - An > introduction to advanced electronic structure theory" by Szabo and Ostlund. > This book doesn't skip any steps in the derivation of the theories, which > most other books do. Also, there are some exercises/examples on HF for HeH+ > in a minimal basis, which can be worked out with pen and paper. --0015175cb4ac8deb9d049b28718d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Sorry for the reply to an old thread, but I thought I would mention that Sz= abo and Ostlund do address CC in chapter 5.

On Wed, Jan 12, 2011 at 3:06 AM, Johannes Johansson johjo76(-)gmail.com <owner-chemistry(_)ccl.net> wrote:
for the basic theory (Hartree-Fock, Moller-= Plesset perturbation theory, CI etc) I know few books that are as detailed = as "Modern Quantum Chemistry - An introduction to advanced electronic = structure theory" by Szabo and Ostlund. This book doesn't skip any= steps in the derivation of the theories, which most other books do. Also, = there are some exercises/examples on HF for HeH+ in a minimal basis, which = can be worked out with pen and paper.=A0

--0015175cb4ac8deb9d049b28718d-- From owner-chemistry@ccl.net Mon Jan 31 17:32:00 2011 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre*univ-provence.fr" To: CCL Subject: CCL: Modeling of biologically-inspired photoactive systems, Marseille, France Message-Id: <-43810-110131130738-15942-QO7nW/TN2E2pZaIukKysoQ ~ server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 31 Jan 2011 19:06:38 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre__univ-provence.fr] Universite' de Provence and Universite' Paris-Sud are pleased to announce the 1st European workshop entitled "Modeling of biologically-inspired photoactive systems". It will be held in Marseille, France, from March 30 to April, 1st 2011. This workshop aims to bring together Europe-based recognized specialists, but also newcomers, young researchers and students that are involved in any theoretical development targeted or possibly applicable to the modeling of bio-photochemistry. Besides the presentation of well-established methods and their applications, the participants will be asked to present their up-to-date theoretical developments and to give their opinions about the future of such an intense research area, in terms of experimental-theoretical collaborations, needed new methodologies, ... The number of participants is limited to 50. Reduced fees are available to students and postdoctoral researchers (limited to 20 registrations). Deadline for registration and oral communication submission is march 1st. A poster session will be open to all the participants. More information is available at http://sites.univ-provence.fr/lcp-ct/biophotochem/ See you in Marseille! Prof. Isabelle Demachy (Universite' Paris-Sud) and Dr. Nicolas Ferre' (Universite' de Provence) From owner-chemistry@ccl.net Mon Jan 31 21:50:00 2011 From: "Dr David N Haney haney[a]edusoft-lc.com" To: CCL Subject: CCL: Calculating surface hydrophobicity Message-Id: <-43811-110131214751-25173-H5DZrthGd40N0uTeLP/Tng^server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 31 Jan 2011 18:47:25 -0800 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney]=[edusoft-lc.com] Sumitro, This problem has been studied extensively for many years in the software HINT by EduSoft (www.edusoft-lc.com). The method assigns a "hydropathy" value to each atom based on fragment data of Abraham and Leo (1987, Proteins). One of the publications describing HINT is in Journal of Computer-Aided Molecular Design (2001), vol 15, 381-393. You can find more publications at http://www.edusoft-lc.com/hint/hintpubs.html. More recently HINT has been used to estimate free energy changes and effects of bound water molecules (to protein). On Sun, Jan 30, 2011 at 10:28:02PM -0500, Sumitro Harjanto sharjanto[*]i2r.a-star.edu.sg wrote: > > Sent to CCL by: "Sumitro Harjanto" [sharjanto::i2r.a-star.edu.sg] > Hi , > > I want to calculate the surface hydrophobicity of a protein molecule, but so > far I only manage to use atomic partial charges as the estimate of the surface > hydrophobicity, anyone can provide me some insight on how well is that as an > estimate..? > > Also, it will be great help if anyone knows of any software/webtools/ that > calculates surface hyrdrophobicity of protein, which generates some kind of > grid output file. Thanks! > > (btw, my input file is in .pdb format) > > Cheers, > Sumitro> -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney===edusoft-lc.com # ################# #####################