From owner-chemistry@ccl.net Fri Jun 12 00:41:01 2009 From: "Yutao Yue yutao.yue---gmail.com" To: CCL Subject: CCL: pH-dependent ab-initio calculations Message-Id: <-39501-090612002956-764-Rg7AWE5wGrpbwAxLYO2/Jw,server.ccl.net> X-Original-From: Yutao Yue Content-Type: multipart/alternative; boundary=00163646d8e6cb8540046c1f1371 Date: Fri, 12 Jun 2009 00:23:58 -0400 MIME-Version: 1.0 Sent to CCL by: Yutao Yue [yutao.yue .. gmail.com] --00163646d8e6cb8540046c1f1371 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thanks to everybody. If anybody is also interested in pH/pKa dependent molecule/protein reactivities, and wants a good explanation of the basics, here is a nicely organized and clearly explained review that I am reading: Analyzing enzymatic pH activity profiles and protein titration curves using structure-based pKa calculations and titration curve fitting, *Nielsen JE , Methods Enzymol. 2009;454:233-58*the PubMed link: http://www.ncbi.nlm.nih.gov/pubmed/19216929 Good luck to everybody. YT On Mon, Jun 8, 2009 at 5:47 AM, James Justin Robinson james.robinson: prosonix.co.uk wrote: > > Sent to CCL by: "James Justin Robinson" [james.robinson],[prosonix.co.uk] > Hi Mahmoud, > > I heartily recommend you grab papers written by Liptak and Shields, there > is debate over the entropy related to solvation of a proton in water. The > solvation methods you use will affect the result. I have used Cosmo-RS as > suggested by Andreas and you should ask more of him and the software > developed that uses Cosmo-RS. > > james> > > --00163646d8e6cb8540046c1f1371 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks to everybody. If anybody is also interested in pH/pKa dependent mole= cule/protein reactivities, and wants a good explanation of the basics, here= is a nicely organized and clearly explained review that I am reading:

Analyzing enzymatic pH activity profiles and protein titration curves using= structure-based pKa calculations and titration curve fitting,=A0Nielsen JE,=A0<= span class=3D"Apple-style-span" style=3D"font-weight: normal; ">Methods Enzymol.=A02009;454:233-58=

the PubMed link:

Good luck to everybody.

YT


On Mon, Jun 8, 2009 at 5:47 AM, Jam= es Justin Robinson james.robinson:prosoni= x.co.uk <owner-chemistry.,.ccl.net> wrote:

Sent to CCL by: "James Justin Robinson" [james.robinson],[prosonix.co.uk]
Hi Mahmoud,

I heartily recommend you grab papers written by Liptak and Shields, there i= s debate over the entropy related to solvation of a proton in water. The so= lvation methods you use will affect the result. I have used Cosmo-RS as sug= gested by Andreas and you should ask more of him and the software developed= that uses Cosmo-RS.

james



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--00163646d8e6cb8540046c1f1371-- From owner-chemistry@ccl.net Fri Jun 12 07:16:01 2009 From: "Marek Maly marek.maly : ujep.cz" To: CCL Subject: CCL: PRINCIPAL - QUESTION Message-Id: <-39502-090612070930-7784-OBtMms360IT1noGRDqvxNw+*+server.ccl.net> X-Original-From: "Marek Maly" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-2 Date: Fri, 12 Jun 2009 13:09:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Marek Maly" [marek.maly()ujep.cz] Dear all, I have following problem: I have simulated complex of PPI dendrimer decorated with maltose (neutral molecule) and ssDNA (with the total charge -24) (time length 13 ns). I have obtained nice complex. From the snaps (obtainet at 12.5 and 13.0 ns of the simulation - please see here http://physics.ujep.cz/~mmaly/fig/ ) is clear that it is really stable complex. (I also made RMSD,Rg analysis) This complexation was moreover recently confirmed also experimentally. Unfortunately from the mm_PBSA analysis of the last nanosecond I have obtained positive value for mean binding energy (dG = 38,5 kcal/mol - please see below). So I have just simple but principal question. It is THEORETICALLY possible STABLE complex where favourable decreas in enthalpy after binding is more than compensate by entropy penalty because of the unfavourable loss in entropy after complexation ?. I thought that this is not possible, but now I don't know ... Thank you very much in advance for any comment or relevant article/(www link) redirection. With the best regards Marek mm_PBSA analysis - one trajectory approach (last 1ns - 20frames in total) --------------------------------------------------- dH - mean value -41,78 <<<- dH - standard deviation 12,67 TdS - mean value -80,28 <<<- TdS - standard deviation 18,23 dG = dH - TdS - mean value 38,50 <<<- dG = dH - TdS - standard deviation 22,20 -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ From owner-chemistry@ccl.net Fri Jun 12 14:06:01 2009 From: "aneesh cna aneeshcna]~[gmail.com" To: CCL Subject: CCL: Regarding force constant matrix Message-Id: <-39503-090612140236-13805-rgdtRW78hppdn7FkVAd1QQ a server.ccl.net> X-Original-From: "aneesh cna" Date: Fri, 12 Jun 2009 14:02:32 -0400 Sent to CCL by: "aneesh cna" [aneeshcna+/-gmail.com] Dear CCL users, I would like to calculate the force constant for bond and angle.I am using gussian03 pachkage forc QM calculation. Is it correct with using the force constant from force constant in internal coordinate matrix ?. How can I get seperately the bond and angle force constant from the force constant matrix?. For example,below is force constant in internal coordinate matrix for a water molecule . Force constants in internal coordinates: 1 2 3 1 0.612864D+00 2 -0.636590D-02 0.612864D+00 3 0.262746D-01 0.262746D-01 0.184953D+00 Is this 1-3 numbers correspoinds to the three atoms in the input Z-matrix? Output also wrriten the force constant in catersian coordinate as shown below.. Force constants in Cartesian coordinates: 1 2 3 4 5 1 0.615710D+00 2 0.000000D+00 0.121662D-03 3 -0.126839D+00 0.000000D+00 0.705542D+00 4 -0.609095D-01 0.000000D+00 -0.588957D-01 0.573191D-01 5 0.000000D+00 -0.608311D-04 0.000000D+00 0.000000D+00 0.418506D-04 6 0.108386D-01 0.000000D+00 -0.599717D+00 -0.152672D-03 0.000000D+00 7 -0.554801D+00 0.000000D+00 0.185735D+00 0.359039D-02 0.000000D+00 8 0.000000D+00 -0.608311D-04 0.000000D+00 0.000000D+00 0.189806D-04 9 0.116000D+00 0.000000D+00 -0.105826D+00 0.590483D-01 0.000000D+00 6 7 8 9 6 0.613253D+00 7 -0.106860D-01 0.551210D+00 8 0.000000D+00 0.000000D+00 0.418506D-04 9 -0.135356D-01 -0.175049D+00 0.000000D+00 0.119361D+00 What this 1-9 numbers meant for? How can I get the correct units for force constant, i.e., kJ/mol/A**2 for bond and kJ/mol/rad**2 for angle?. Can anyone heplp me in figure out this problems? Thanks in advance Aneesh aneeshcna-,-gmail.com From owner-chemistry@ccl.net Fri Jun 12 14:44:00 2009 From: "Vincent.Leroux-*-loria.fr" To: CCL Subject: CCL: PRINCIPAL - QUESTION Message-Id: <-39504-090612085418-13100-2VB+KcqBvylwr9aqv9W7zQ]~[server.ccl.net> X-Original-From: Vincent.Leroux[*]loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Fri, 12 Jun 2009 14:54:07 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux*o*loria.fr Hi Marek, If you have been using implicit solvation, the resulting =20 approximations might just be so harmful that estimating the free =20 energy of binding in such a large and polar complex is a complete =20 waste of time. If this is the case, if you want more realistic values, =20 you should bury your system into a large waterbox, neutralize it with =20 counterions and restart MD with the appropriate parameters. Regards, VL "Marek Maly marek.maly : ujep.cz" a =C3=A9crit=C2= =A0: > > Sent to CCL by: "Marek Maly" [marek.maly()ujep.cz] > Dear all, > > I have following problem: > > I have simulated complex of PPI dendrimer decorated with maltose > (neutral molecule) and ssDNA (with the total charge -24) (time =20 > length 13 ns). > I have obtained nice complex. From the snaps (obtainet at 12.5 and > 13.0 ns of the simulation - please see here =20 > http://physics.ujep.cz/~mmaly/fig/ ) > is clear that it is really stable complex. (I also made > RMSD,Rg analysis) This complexation was moreover recently confirmed =20 > also experimentally. > > Unfortunately from the mm_PBSA analysis of the last nanosecond I have > obtained positive value for mean binding energy (dG =3D 38,5 kcal/mol =20 > - please see below). > > So I have just simple but principal question. > > > It is THEORETICALLY possible STABLE complex where favourable decreas in > enthalpy after binding is more than compensate > by entropy penalty because of the unfavourable loss in entropy after > complexation ?. > > I thought that this is not possible, but now I don't know ... > > Thank you very much in advance for any comment or relevant =20 > article/(www link) redirection. > > With the best regards > > Marek > > > mm_PBSA analysis - one trajectory approach (last 1ns - 20frames in total) > --------------------------------------------------- > dH - mean value=09=09=09-41,78 <<<- > dH - standard deviation=09=09 12,67 > TdS - mean value =09=09=09-80,28 <<<- > TdS - standard deviation=09=09 18,23 > dG =3D dH - TdS - mean value =09=09 38,50 <<<- > dG =3D dH - TdS - standard deviation =09 22,20 > > > > From owner-chemistry@ccl.net Fri Jun 12 17:14:00 2009 From: "Marek Maly marek.maly^^^ujep.cz" To: CCL Subject: CCL: PRINCIPAL - QUESTION Message-Id: <-39505-090612170625-28908-Usu0dEtqcuEEaU8x86m3Dw_-_server.ccl.net> X-Original-From: "Marek Maly" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-2 Date: Fri, 12 Jun 2009 23:06:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Marek Maly" [marek.maly---ujep.cz] Hi Vincent, thank you for your response ! I forget to notice that simulation which I have described was done in explicit water with contraions.... Best, Marek Dne Fri, 12 Jun 2009 14:54:07 +0200 Vincent.Leroux-*-loria.fr napsal/-a: > > Sent to CCL by: Vincent.Leroux*o*loria.fr > Hi Marek, > > If you have been using implicit solvation, the resulting approximations > might just be so harmful that estimating the free energy of binding in > such a large and polar complex is a complete waste of time. If this is > the case, if you want more realistic values, you should bury your system > into a large waterbox, neutralize it with counterions and restart MD > with the appropriate parameters. > > Regards, > VL > > > > "Marek Maly marek.maly : ujep.cz" a écrit : > >> >> Sent to CCL by: "Marek Maly" [marek.maly()ujep.cz] >> Dear all, >> >> I have following problem: >> >> I have simulated complex of PPI dendrimer decorated with maltose >> (neutral molecule) and ssDNA (with the total charge -24) (time length >> 13 ns). >> I have obtained nice complex. From the snaps (obtainet at 12.5 and >> 13.0 ns of the simulation - please see here >> http://physics.ujep.cz/~mmaly/fig/ ) >> is clear that it is really stable complex. (I also made >> RMSD,Rg analysis) This complexation was moreover recently confirmed >> also experimentally. >> >> Unfortunately from the mm_PBSA analysis of the last nanosecond I have >> obtained positive value for mean binding energy (dG = 38,5 kcal/mol - >> please see below). >> >> So I have just simple but principal question. >> >> >> It is THEORETICALLY possible STABLE complex where favourable decreas in >> enthalpy after binding is more than compensate >> by entropy penalty because of the unfavourable loss in entropy after >> complexation ?. >> >> I thought that this is not possible, but now I don't know ... >> >> Thank you very much in advance for any comment or relevant >> article/(www link) redirection. >> >> With the best regards >> >> Marek >> >> >> mm_PBSA analysis - one trajectory approach (last 1ns - 20frames in >> total) >> --------------------------------------------------- >> dH - mean value -41,78 <<<- >> dH - standard deviation 12,67 >> TdS - mean value -80,28 <<<- >> TdS - standard deviation 18,23 >> dG = dH - TdS - mean value 38,50 <<<- >> dG = dH - TdS - standard deviation 22,20 >> >> >> >> > > > > -> > > > __________ Informace od NOD32 4051 (20090504) __________ > > Tato zprava byla proverena antivirovym systemem NOD32. > http://www.nod32.cz > > -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/