From owner-chemistry@ccl.net Mon Jul 6 09:09:01 2009 From: "Kefa Lu kefa.lu[-]gmail.com" To: CCL Subject: CCL: pKa calculation of strong acid Message-Id: <-39692-090706032616-11384-POE+HMywT4oVjPdm1VBwFw^-^server.ccl.net> X-Original-From: "Kefa Lu" Date: Mon, 6 Jul 2009 03:26:12 -0400 Sent to CCL by: "Kefa Lu" [kefa.lu/a\gmail.com] Hi,all, Does anybody have experience or idea about the pKa calculation of a strong acid like HCl in water and protein? Thanks. Kefa From owner-chemistry@ccl.net Mon Jul 6 09:44:01 2009 From: "Kefa Lu kefa.lu%gmail.com" To: CCL Subject: CCL: pKa calculation of strong acid Message-Id: <-39693-090705195443-14564-Bl9ALGYG3m+t8Zz/bUm/ng a server.ccl.net> X-Original-From: "Kefa Lu" Date: Sun, 5 Jul 2009 19:54:39 -0400 Sent to CCL by: "Kefa Lu" [kefa.lu%gmail.com] Hi, all, Does anybody have any experience or idea about pKa calculation of a strong acid like HCl in water and in protein? Thanks! Kefa From owner-chemistry@ccl.net Mon Jul 6 10:35:01 2009 From: "Brunsteiner, Michael micb!A!uic.edu" To: CCL Subject: CCL: atom types of OPLS-AA Message-Id: <-39694-090705170706-20079-5s0h/w8IAthsSxOVBjp/GQ!=!server.ccl.net> X-Original-From: "Brunsteiner, Michael" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 5 Jul 2009 16:00:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Brunsteiner, Michael" [micb#uic.edu] On Sun, July 5, 2009 05:10, Chaofu Wu xiaowu759()hotmail.com wrote: > > Sent to CCL by: "Chaofu Wu" [xiaowu759]~[hotmail.com] > Dear ccl users, > I want to study polyamide using OPLS-AA force field. But for the > residues, -CH2-C(=O)-NH-CH2, I can not find suitable atom types for C, > H, atoms on both sides. the atom types are certainly there, for the C and H you can use the corresponding peptide back bone atom types (the ones you'd find, e.g. in a glycine or alanine residue. You might still miss a couple of angle and/or dihedral parameters. For those you can typically use parameters from equivalent fragments in amino acids. You have to be careful though when transferring parameters, at least you'd want to test a couple of short oligomers by comparing energy minimized structures obtained with your OPLS-AA extension and your modeling program to the same structures minimized with some ab-initio program (DFT should be good enough for this purpose. In case you plan to simulate your polymers in aqueous solution you should probably use some kind of solvation model in your ab-initio calcs) You can also use the results from such ab-initio calcs. to improve your atomic charges by calculating ESPD charges (e.g. Gamess-US can do that) How you implement all that in practice depends on the program you use for modeling. I used Gromacs with a range different synthetic organic polymers, such as polysterine, PAA, etc, and the results looked quite reasonable. good luck! mic From owner-chemistry@ccl.net Mon Jul 6 17:00:01 2009 From: "Babak Khalili khalili.babak:-:gmail.com" To: CCL Subject: CCL: Hydrophobicity Message-Id: <-39695-090706165446-18948-6pHpHtpOYFe8DRe/sX48wA###server.ccl.net> X-Original-From: Babak Khalili Content-Type: multipart/alternative; boundary=00504502b079b07fac046e0fb61d Date: Tue, 7 Jul 2009 01:24:35 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak(_)gmail.com] --00504502b079b07fac046e0fb61d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear al How can I calculate the hydrophobicity of a peptide? Thank you for your earliest attention Babak khalili Haddad --00504502b079b07fac046e0fb61d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear al
How can I calculate the hydrophobicity of a peptide?

Thank you for your earliest attention
Babak khalili Haddad
--00504502b079b07fac046e0fb61d-- From owner-chemistry@ccl.net Mon Jul 6 20:01:01 2009 From: "Hai-Bin Li lihb734+*+yahoo.com" To: CCL Subject: CCL:G: dipole moment of excited states Message-Id: <-39696-090706195812-25369-hnR6G9kgjLoPyytDwVW8Og^server.ccl.net> X-Original-From: "Hai-Bin Li" Date: Mon, 6 Jul 2009 19:58:09 -0400 Sent to CCL by: "Hai-Bin Li" [lihb734,yahoo.com] Dear all subscribers: Recently, I have read a excellent refenrence published in J. Phys. Chem. A 2005, 109, 9760-9766. The author present his results about dipole moment of T1, T2, T3 and S1, S2, S3 et. al excited states using Gaussian98 in TABLE 3. So, I have a question on how to calculate these EXCITED STATES' dipole moment? Which keyword or option or IOP should invoke to attain these? Many thanks to your kind reply. Hai-Bin Li Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University changchun, Jilin, 130024 PR CHINA E-mail: lihb734]~[nenu.edu.cn; lihb734]~[yahoo.com http://www.nenu.edu.cn From owner-chemistry@ccl.net Mon Jul 6 20:36:00 2009 From: "Chaofu Wu xiaowu759.::.hotmail.com" To: CCL Subject: CCL: atom types of OPLS-AA Message-Id: <-39697-090706203320-7738-R5yhVjSN3QD3cGxMFS2cAA::server.ccl.net> X-Original-From: "Chaofu Wu" Date: Mon, 6 Jul 2009 20:33:16 -0400 Sent to CCL by: "Chaofu Wu" [xiaowu759*hotmail.com] Dear Micheael, Thank you very much for this reply. I think, you have provided adequate information for coping with my problem. However, I have difficuty in using DFT like methods for obtaining the missing parameters. In practice, I use gromacs to do MD simulations and the practical problem is no default ryckaert-bell. types for the dihedrals -CH2-C(=O)-NH-CH2- as the grompp complains. So I guess it must be wrong atom types assigned that causes that problem. Could you tell me what are suitable atom types for C, H, atoms on both sides in terms of OPLS-AA in GROMACS format? Notes: I find an article [ J. Phys. Chem. B, 2007, 111 (36), pp 1065110664] in which detailed parameters are represented for the similar system. I want to use the parameters reported for the dihedrals -CH2-C(=O)-NH-CH2-, but I find there is something wrong or unsuitable with the atom types. Can I use such parameters, anyway? Sincerely, Chaofu Wu, Dr. > From: owner-chemistry-.-ccl.net > To: xiaowu759-.-hotmail.com > Subject: CCL: atom types of OPLS-AA > Date: Sun, 5 Jul 2009 16:00:16 -0500 > > > Sent to CCL by: "Brunsteiner, Michael" [micb#uic.edu] > On Sun, July 5, 2009 05:10, Chaofu Wu xiaowu759()hotmail.com wrote: > > > > Sent to CCL by: "Chaofu Wu" [xiaowu759]~[hotmail.com] > > Dear ccl users, > > I want to study polyamide using OPLS-AA force field. But for the > > residues, -CH2-C(=O)-NH-CH2, I can not find suitable atom types for C, > > H, atoms on both sides. > > the atom types are certainly there, for the C and H you can > use the corresponding peptide back bone atom types (the ones > you'd find, e.g. in a glycine or alanine residue. You might > still miss a couple of angle and/or dihedral parameters. For > those you can typically use parameters from equivalent fragments > in amino acids. You have to be careful though when transferring > parameters, at least you'd want to test a couple of short > oligomers by comparing energy minimized structures obtained with > your OPLS-AA extension and your modeling program to the same > structures minimized with some ab-initio program (DFT > should be good enough for this purpose. In case you plan to > simulate your polymers in aqueous solution you should probably use > some kind of solvation model in your ab-initio calcs) > You can also use the results from such ab-initio calcs. to > improve your atomic charges by calculating ESPD charges (e.g. > Gamess-US can do that) > > How you implement all that in practice depends on the program > you use for modeling. I used Gromacs with a range different > synthetic organic polymers, such as polysterine, PAA, etc, > and the results looked quite reasonable. > > good luck! > mic