From owner-chemistry@ccl.net Thu Dec 4 01:27:01 2008 From: "Raphael Ribeiro raphaelri..hotmail.com" To: CCL Subject: CCL: translational entropy in solvent Message-Id: <-38237-081204012402-11806-hzCUM/j4bSjDwyhwPGmofA-x-server.ccl.net> X-Original-From: "Raphael Ribeiro" Date: Thu, 4 Dec 2008 01:23:58 -0500 Sent to CCL by: "Raphael Ribeiro" [raphaelri*|*hotmail.com] Quantum chemistry packages usually calculate translational entropy and the other thermal effects using the ideal gas approximation, even if you do the optimization-hessian task using a solvent model. In general, the free solvation energy calculated in implicit solvent models accounts only for polarization effects. It may be calculated as the work done in isothermal conditions to polarize(or charge) the system, or as an electrostatic potential energy. Some of the implicit models also include non-eletrostatic contributions (cavitation, dispersion and structure effects). This free energy of solvation is defined as the difference between the free energy of the system in the solvated phase and in the gas phase. It is not correct to add translational entropy in the free energy of solvation. The free energy of solvation, if calculated accurately, should include the difference between the translational entropy of the two phases and also all of the other components of entropy and enthalpy. The only problem is that in most of the cases you can't calculate it in an accurate way. And the reason is quite obvious, the solvent in the real world isn't a continuous medium. The procedures you outlined below are in my view not correct. The components(translational,rotational,etc) of enthalpy and especially entropy of a system calculated in solvated phases using implicit solvents are not accurate at all, as your phase space is very limited (most of the phase space comes from the solvent and a continuous solvent does not have any degree of freedom). So you have to be very careful when using this kind of information. Implicit solvent models were made in a way the best we can get from them is the free energy of solvation, and some of them are even parametrized to give precise free energy of solvations. Any other information given when you use these models (components of entropy,etc) in most of the times does not mean anything. Raphael Ribeiro > From: owner-chemistry!A!ccl.net > To: raphaelri!A!hotmail.com > Subject: CCL: translational entropy in solvent > 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 Thu Dec 4 02:01:01 2008 From: "Neha Gandhi n.gandhiau[a]gmail.com" To: CCL Subject: CCL: Cremer-pople parameters Message-Id: <-38238-081204012944-13323-/e5e4SZzl+iOtqjkKKcycA!^!server.ccl.net> X-Original-From: "Neha Gandhi" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 4 Dec 2008 13:38:54 +0800 MIME-Version: 1.0 Sent to CCL by: "Neha Gandhi" [n.gandhiau===gmail.com] Hi, I am looking for a program which can help me to calculate Cremer-Pople ring puckering parameters for pyranose or in general six member rings > from the AMBER trajectories. I heard about Mark Foster's program QCPE, but its hard to visualise. I am grateful for you reply, Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 From owner-chemistry@ccl.net Thu Dec 4 02:49:00 2008 From: "Andreas Klamt klamt!=!cosmologic.de" To: CCL Subject: CCL: translational entropy in solvent Message-Id: <-38239-081204024042-24559-Eb/uImp1s5tFeD/dUP9sFA|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 04 Dec 2008 08:40:25 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt*cosmologic.de] Dear Luis, yes, the issue has been previously discussed, but it it important and=20 thus comes again and again: 1) We computational chemists are lucky to be able to have the rather=20 exact equations for the (translational, rotational, and vibrational)=20 free energy of molecules in the ideal gas phase (apart from=20 anharmonicity corrections and some problems with rotor modes). This ia a = clear and nice reference state. 2) There are solvation models which allow us to reasonable estimate=20 dG_solv for almost any compound in almost any solvent. We have just=20 recently proven on an external data set (originally collected by Cramer=20 and Truhlar in context of their SM8 model) of ~2400 exp. dG_solv values=20 for a wide variety of molecules in a wide variety of solvents that our=20 COSMO-RS (COSMOtherm implementation) can calculate dG_solv with an=20 average error of 0.48 kcal/mol. Most likely the method is even better=20 than that, because the experimentatl data set included a lot of=20 experimental data which appear to be more than questionable, but we did=20 not exclude any of them for the sake of comparability. (The study is=20 submitted for publication). 3) Now, let us assume that the error of a good solvation model is 0.4=20 kcal/mol at room temperature, which is just only a factor of 2 in the=20 partition function (and in the Henry's Law constant, partial pressure,=20 =2E..) In the calculation of a reaction free energy we will most likely = benefit from some compensation of errors on the educt and product side.=20 Then this is most likely accurate enough for not being responsible for=20 significant errors in calculations of reaction free energies. All other=20 errors arising from quantum chemistry, and even from the approximations=20 in the rotational, and vibrational free energy contributions are most=20 likely larger than the error coming from good solvation models. Conclusion: The translational, rotational, and vibrational free energy=20 conributions of solvation are apparently well parameterized into=20 quantitative solvation models. Hence a combination of as good as=20 possible gas phase thermodynamics (i.e. free energy calulations) with a=20 quantitative solvation model is the best you can do in the moment. Don't = start to try to calculate parts of the translational, rotational, and=20 vibrational free energy conributions in solution. This will lead to=20 double counting of effects already implicitly taken into account in=20 solvation models. Andreas P.S.: For most solvation models this is true at room temperature. To my=20 best knowledge my COSMO-RS method is the only imlicit solvation model=20 which derives the free energy of solavtion from a partition functions=20 and separates entropy and enthalpy, and which is validated=20 simultaneously on free enrgies and enthalpies of solvation, and on=20 solvation properties at varying temperature in the range of -100 =B0C to = ~=20 300=B0C. Luis M Sim n lsimon^usal.es schrieb: > Sent to CCL by: "Luis M Sim n" [lsimon|-|usal.es] > Many quantum chemistry packages include implicit solvation models, such= as PCM, CPCM, COSMO,=20 > etc. Nevertheless, even when the optimization was done using any of tho= se solvation models, I have=20 > observed that the thermal contributions to delta G are calculated assum= ing that the molecules are in=20 > the gas phase. Therefore, the translational entropy is overestimated (s= ee, for example, C. Hunter,=20 > ACIE, 43, 5310-5324, 2004).=20 > > There are models that can estimate this translational entropy in soluti= on (Warshell et al.,=20 > J.Phys.Chem.B, 104, 4578-4584, 2000), but unfortunately these are not s= traightforward to implement,=20 > and computational requirements might exceed our possibilities.=20 > > On the other side, I have seen that implicit solvent calculations many = times offers a "free solvation=20 > energy". I do not know if, in that free solvation energy, the translati= onal energy is, somehow,=20 > evaluated and included, or if it just accounts for cavitation and polar= ization contributions. > > My question is: is it correct to add up the translational estropy calcu= lated assuming gas phase=20 > behaviour to that free solvation energy? Should not it be more correct = if the vibrational or even=20 > rotational contributions are included in deltaG calculations but transl= ational contribution is excluded?=20 > Does anyone knows any easy method for, approximately, account for the t= ranslational entropy in=20 > solution, in case that have to be added to the vibrational and rotation= al contributions? > > Sorry if that issue have previously been discussed. > > > > -=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 chang= e> > Subscribe/Unsubscribe:=20> > Job: http://www.ccl.net/jobs=20= > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: searc= h)> > > > > =20 --=20 -------------------------------------------------------------------------= - Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt[-]cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------= - COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------= - Please note our COSMO-RS Symposium in 2009=20 (For details see: http://www.cosmologic.de/Symposium/symposium.html) From owner-chemistry@ccl.net Thu Dec 4 04:13:00 2008 From: "Tristan Youngs t.youngs---qub.ac.uk" To: CCL Subject: CCL: Cremer-pople parameters Message-Id: <-38240-081204041158-2506-cpWdPYH63L+A084ENr3Iow|*|server.ccl.net> X-Original-From: Tristan Youngs Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 04 Dec 2008 09:11:46 +0000 MIME-Version: 1.0 Sent to CCL by: Tristan Youngs [t.youngs]~[qub.ac.uk] A method to calculate IUPAC ring conformations (via the mapping of conformational space onto a sphere) is described in: Berces, A.; Whitfield, D. M.; Nukada, T. Tetrahedron 2001, 477-491. The necessary code for generating the basic descriptive conformational parameters from the ring torsions (rather than the atomic coordinates) is fairly simple using the method outlined in the paper. Cheers, Tris. Neha Gandhi n.gandhiau[a]gmail.com wrote: > Sent to CCL by: "Neha Gandhi" [n.gandhiau===gmail.com] > Hi, > > I am looking for a program which can help me to calculate Cremer-Pople > ring puckering parameters for pyranose or in general six member rings > >> from the AMBER trajectories. I heard about Mark Foster's program QCPE, >> > but its hard to visualise. > > I am grateful for you reply, > > Regards, > Neha Gandhi, > School of Biomedical Sciences, > Curtin University of Technology, > GPO Box U1987 Perth, > Western Australia 6845> > > -- Dr. T. Youngs (t.youngs,,qub.ac.uk) Atomistic Simulation Centre Old Physics Building Queen's University Belfast Belfast, BT7 1NN, N.I. From owner-chemistry@ccl.net Thu Dec 4 05:26:01 2008 From: "Jean-Christophe Poully poully[-]galilee.univ-paris13.fr" To: CCL Subject: CCL:G: ONIOM TDDFT charge multiplicity error Message-Id: <-38241-081204050653-29535-AWe/xhcq+vqi7EIEaN5r5A##server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Thu, 04 Dec 2008 11:06:18 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully . galilee.univ-paris13.fr] Dear Justine, The 3 pairs of numbers relative to spin and=20 multiplicity represent the spin and multiplicity=20 of, respectively, the real system at the low=20 level of calculation (e.g. the entire molecule),=20 the model system (the atoms included in the high=20 layer) at the high level of calculation, and=20 again the model system but at the low level. Thus=20 the two last pairs must be the same numbers, in=20 your example you should try to put 3 2 -2 1 -2 1=20 or 3 2 5 2 5 2, depending on your system and the=20 calculation you want to carry out. Hope it helps! JC Poully At 01:08 04/12/2008, you wrote: >Sent to CCL by: "Justine A Shaw" [j-shaw_+_northwestern.edu] >Dear readers, >I am trying to run an ONIOM TDDFT 2 level=20 >calculation and I have run into a difficulty=20 >specifying the correct charge/multiplicity for=20 >the various levels in the system. Here is an example of my input file: > >%chk=3Dfilename.chk > >%mem=3D500MB ># ONIOM(B3LYP/GenECP/Auto TD=3D(NStates=3D20):AMBER) ># IOp(5/94=3D0) Geom=3DConnectivity ># scf=3D(maxcycle=3D1000, tight) int=3Dultrafine > >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=20 >immediately states that an incorrect=20 >charge/multiplicity is specified. However, if=20 >I change my charge /multiplicty line to 3 1 -2=20 >1 5 1 the calculation will run for a while then output the following: > > MMInit generated parameter data with length=20 > LenPar=3D 24310. > Standard basis: Dummy (5D,=20 > 7F) > The combination of multiplicity 1 and 91=20 > electrons is impossible. > Error termination via Lnk1e in=20 > /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=20 > seconds. > File lengths (MBytes): RWF=3D 2032=20 > Int=3D 0 D2E=3D 0 Chk=3D 376 Scr=3D 8 > >I do not understand how it comes up with an=20 >electron count of 91? My high level region=20 >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 >************************************* > > > >-=3D This is automatically added to each message by the mailing script =3D-Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Thu Dec 4 06:15:00 2008 From: "Sangeetha Vimal srdshigella _ gmail.com" To: CCL Subject: CCL: How to model insertions in proteins? Message-Id: <-38242-081204061325-25492-cqZwfoLzXGZ0Q01TJPbBNA]^[server.ccl.net> X-Original-From: "Sangeetha Vimal" Date: Thu, 4 Dec 2008 06:13:21 -0500 Sent to CCL by: "Sangeetha Vimal" [srdshigella[*]gmail.com] Hi all, I am modeling a protein based on multiple structural alignment of templates. There is an insertion region (of 10 residues) in the target protein, for which there are no homologues. Modeler assigns the insertion region as loop as there is no template segment. I tried predicting the secondary structure of this insertion region (which seems to be beta-sheet). So how can I model this segment? Can someone address this problem? Any help is sincerely appreciated. Thanks Sangeetha. From owner-chemistry@ccl.net Thu Dec 4 07:34:01 2008 From: "James J Robinson james.robinson_._prosonix.co.uk" To: CCL Subject: CCL: translational entropy in solvent Message-Id: <-38243-081204073142-29061-X1AMlWrp2KSLhTq+Noxoyw!=!server.ccl.net> X-Original-From: "James J Robinson" Date: Thu, 4 Dec 2008 07:31:38 -0500 Sent to CCL by: "James J Robinson" [james.robinson : prosonix.co.uk] Computational chemistry is concerned with the examination and interpretation of applied maths, run on computers that also produces very nice images. The real test surely would be to compare experiment and comp results. A good test to examine your solvatio errors, might be to examine something that can empiricially determined, eg pka. It is too easy and tempting to get immersed into equations, experiment should also form part of your examination. See work of Cramer, Thrular, Klamt, Liptak and Shields. Dr James J Robinson Senior Scientist Prosonix Ltd Magdalen Centre Robert Robinson Avenue Oxford Science Park Oxford, Oxon. OX4 4GA, UK. +44(0) 1865 784243 From owner-chemistry@ccl.net Thu Dec 4 10:43:00 2008 From: "Didier ROGNAN didier.rognan[a]pharma.u-strasbg.fr" To: CCL Subject: CCL: scPDB 2008 Message-Id: <-38244-081204104118-12592-WCEfqx7TYwjIc6ieQoo9kg|,|server.ccl.net> X-Original-From: "Didier ROGNAN" Date: Thu, 4 Dec 2008 10:41:14 -0500 Sent to CCL by: "Didier ROGNAN" [didier.rognan-*-pharma.u-strasbg.fr] Dear CCLers, I am happy to announce the 2008 release of the scPDB database of druggable binding sites. The web interface has been completely modified and allows a simple but efficient mining of druggable protein-ligand PDB complexes by mixing queries on ligands, proteins and binding modes. The database is available at: http://bioinfo-pharma.u-strasbg.fr/scPDB The database currently contains 5278 protein-ligand complexes with 1766 unique proteins and 2393 unique ligands in corrected mol2 format. Feel free to use it and send comments to: Dr. Didier Rognan CNRS UMR 7175-LC1 Bioinformatics of the Drug Institut Gilbert Laustriat F-67400 Illkirch phone: +33.3.90244235 fax: +33.3.90244310 email: didier.rognan|,|pharma.u-strasbg.fr From owner-chemistry@ccl.net Thu Dec 4 11:25:02 2008 From: "Mahmoud A. A. Ibrahim m.ibrahim1982,+,yahoo.com" To: CCL Subject: CCL: How to model insertions in proteins? Message-Id: <-38245-081204081602-18673-mIkSbS9TapCqFKO7VatWDA{=}server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-297972749-1228393272=:88255" Date: Thu, 4 Dec 2008 04:21:12 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982 ~ yahoo.com] --0-297972749-1228393272=:88255 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sangeetha I am not expert in this area and nowadays I am reading about it. But I thin= k you can build a loop by using Swiss PDB Viewer, but bear in mind the maxi= mum lenght for the loop is 20 amino acid and the minimum is 3 amino acids. Here (http://spdbv.vital-it.ch/index.html) you will find the swiss program = (it is free) and here (http://spdbv.vital-it.ch/loop_tut.html) you can read= how can insert a loop. If=A0 you have any problem in using the program, don't hesitate to contact = me. sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. Mahmoud.Ibrahim-2=-=postgrad.manchester.ac.uk=20 Home Address=20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt.=20 M.Ibrahim1982=-=yahoo.com=20 Mobile Phone No.: +20102554083=20 Land Phone No.: +20226635916=20 Fax No.: +20862342601 --- On Thu, 12/4/08, Sangeetha Vimal srdshigella _ gmail.com wrote: > From: Sangeetha Vimal srdshigella _ gmail.com Subject: CCL: How to model insertions in proteins? To: "Ibrahim, Mahmoud Arafat Abd El-Hamid " Date: Thursday, December 4, 2008, 1:13 PM Sent to CCL by: "Sangeetha Vimal" [srdshigella[*]gmail.com] Hi all, I am modeling a protein based on multiple structural alignment of templates= .. There is an insertion region (of 10 residues) in the target protein, for wh= ich there are no homologues. Modeler assigns the insertion region as loop as th= ere is no template segment. I tried predicting the secondary structure of this insertion region (which seems to be beta-sheet). So how can I model this segment?=20 Can someone address this problem? =20 Any help is sincerely appreciated. Thanks Sangeetha. -=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=20http://www.ccl.net/spammers.txt=0A=0A=0A --0-297972749-1228393272=:88255 Content-Type: text/html; charset=us-ascii
Dear Sangeetha
I am not expert in this area and nowadays I am reading about it. But I think you can build a loop by using Swiss PDB Viewer, but bear in mind the maximum lenght for the loop is 20 amino acid and the minimum is 3 amino acids.
Here (http://spdbv.vital-it.ch/index.html) you will find the swiss program (it is free) and here (http://spdbv.vital-it.ch/loop_tut.html) you can read how can insert a loop.
If  you have any problem in using the program, don't hesitate to contact me.
sincerely;
M. Ibrahim

Mahmoud A. A. Ibrahim
Current Address
School of Chemistry, University of Manchester,
Oxford Road, Manchester, M13 9PL, United Kingdom.
Mahmoud.Ibrahim-2=-=postgrad.manchester.ac.uk

Home Address
Chemistry Department, Faculty of Science,
Minia University,
Minia 61519,Egypt.
M.Ibrahim1982=-=yahoo.com
Mobile Phone No.: +20102554083
Land Phone No.: +20226635916
Fax No.: +20862342601


--- On Thu, 12/4/08, Sangeetha Vimal srdshigella _ gmail.com <owner-chemistry=-=ccl.net> wrote:
From: Sangeetha Vimal srdshigella _ gmail.com <owner-chemistry=-=ccl.net>
Subject: CCL: How to model insertions in proteins?
To: "Ibrahim, Mahmoud Arafat Abd El-Hamid " <m_arafat82=-=yahoo.com>
Date: Thursday, December 4, 2008, 1:13 PM

Sent to CCL by: "Sangeetha  Vimal" [srdshigella[*]gmail.com]
Hi all,

I am modeling a protein based on multiple structural alignment of templates.
There is an insertion region (of 10 residues) in the target protein, for which
there are no homologues. Modeler assigns the insertion region as loop as there
is no template segment. I tried predicting the secondary
 structure of this
insertion region (which seems to be beta-sheet). So how can I model this
segment? 


Can someone address this problem?
 
Any help is sincerely appreciated.


Thanks


Sangeetha.





--0-297972749-1228393272=:88255-- From owner-chemistry@ccl.net Thu Dec 4 12:01:00 2008 From: "shokofeh massahi massahi_physicalchem]_[yahoo.com" To: CCL Subject: CCL:G: SCF is confused? Message-Id: <-38246-081204085318-29148-nDXR3C1IR8e46YpYpRaNqg,server.ccl.net> X-Original-From: "shokofeh massahi" Date: Thu, 4 Dec 2008 08:53:14 -0500 Sent to CCL by: "shokofeh massahi" [massahi_physicalchem(a)yahoo.com] Hi ccl, I am trying to run a BSSE single-point calculation (counterpoise) using > MP2/aug-cc-pvdz on clusters.THE END OF THE OUTPUT FILE: Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Inconsistent input #3 in SPerMO. Error termination via Lnk1e in C:\G03W\l502.exe at Tue Dec 02 13:55:01 2008. Job cpu time: 0 days 0 hours 8 minutes 17.0 seconds. File lengths (MBytes): RWF= 39 Int= 0 D2E= 0 Chk= 2 Scr= 1 THE INPUT FILE: %mem=300mb %chk=c1c1.chk # MP2/aug-cc-pvdz counterpoise=2 scf=tight > I want to keep the method (MP2) and basis set consistent > between compounds is there anything I can do to make resolve this > problem and allow the calculations to complete normally? > I thank you all in advance for any suggestions, > shokofeh massahi >massah_physicalchem#yahoo.com From owner-chemistry@ccl.net Thu Dec 4 12:34:00 2008 From: "Tom Walsh tom|a|compbio.dundee.ac.uk" To: CCL Subject: CCL:G: Gaussian 03 on CentOS 5.2 Message-Id: <-38247-081204055305-31705-rkzwAY252jNvTmpHSalGBQ-.-server.ccl.net> X-Original-From: Tom Walsh Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 Dec 2008 09:53:46 +0000 MIME-Version: 1.0 Sent to CCL by: Tom Walsh [tom-x-compbio.dundee.ac.uk] Many thanks for the all the helpful responses. It looks like Gaussian will run fine on our setup. Tom From owner-chemistry@ccl.net Thu Dec 4 13:17:01 2008 From: "Rodrigo Souza souzarod21]=[yahoo.com.br" To: CCL Subject: CCL: PCM in Gamess Message-Id: <-38248-081204120347-13368-n27gLqdisGfbGe+aPpAM5Q+/-server.ccl.net> X-Original-From: "Rodrigo Souza" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 4 Dec 2008 14:01:25 -0200 MIME-Version: 1.0 Sent to CCL by: "Rodrigo Souza" [souzarod21 ~~ yahoo.com.br] Dear All, Could somebody help me with the input line for PCM (iefpcm,solvent=water) calculations in Gamess? best wishes Rodrigo O. M. A. de Souza www.olhares.com/rsouza ----- Original Message ----- > From: "James J Robinson james.robinson_._prosonix.co.uk" To: "De Souza, Rodrigo Octavio M. A " Sent: Thursday, December 04, 2008 10:31 AM Subject: CCL: translational entropy in solvent > > Sent to CCL by: "James J Robinson" [james.robinson : prosonix.co.uk] > Computational chemistry is concerned with the examination and > interpretation of applied maths, run on computers that also produces very > nice images. The real test surely would be to compare experiment and comp > results. A good test to examine your solvatio errors, might be to examine > something that can empiricially determined, eg pka. It is too easy and > tempting to get immersed into equations, experiment should also form part > of your examination. See work of Cramer, Thrular, Klamt, Liptak and > Shields. > > Dr James J Robinson > Senior Scientist > Prosonix Ltd > Magdalen Centre > Robert Robinson Avenue > Oxford Science Park > Oxford, Oxon. > OX4 4GA, UK. > +44(0) 1865 784243> > __________________________________________________ Faça ligações para outros computadores com o novo Yahoo! Messenger http://br.beta.messenger.yahoo.com/ From owner-chemistry@ccl.net Thu Dec 4 13:44:00 2008 From: "Ben Webb ben%salilab.org" To: CCL Subject: CCL: How to model insertions in proteins? Message-Id: <-38249-081204123551-6909-I2y4EO06zp0fYAceLc81kg~~server.ccl.net> X-Original-From: Ben Webb Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 04 Dec 2008 09:05:24 -0800 MIME-Version: 1.0 Sent to CCL by: Ben Webb [ben ~ salilab.org] Sangeetha Vimal srdshigella _ gmail.com wrote: > I am modeling a protein based on multiple structural alignment of > templates. There is an insertion region (of 10 residues) in the > target protein, for which there are no homologues. Modeler assigns > the insertion region as loop as there is no template segment. I tried > predicting the secondary structure of this insertion region (which > seems to be beta-sheet). So how can I model this segment? If you want to use Modeller to model your system, you can certainly add secondary structure restraints; see http://salilab.org/modeller/FAQ.html#10 For more information, try the Modeller mailing list at http://salilab.org/modeller/ Ben -- ben(0)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle From owner-chemistry@ccl.net Thu Dec 4 14:39:00 2008 From: "Michael K. Gilson gilson]-[umbi.umd.edu" To: CCL Subject: CCL: translational entropy in solvent Message-Id: <-38250-081204143059-31587-rrywwblmWNfTIHntHQ+4RQ[-]server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 Dec 2008 13:39:59 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson[*]umbi.umd.edu] There can be some real semantic issues here, but I think it's safe to say that a correctly done solvation free energy calculation -- whether implicit or explicit-- will not include a translational contribution associated with the solute. There is no need at all for such a term in a solvation free energy, whether approximate or exact. Here are some more extended (i.e., rambling) comments. The concept of an implicit solvent model can be cleanly derived from statistical thermodynamics. See, e.g., Biophys. J. 72:1047-1069, 1994. (I'm referring to my own work, not because it is necessarily best, but because I'm most familiar with it.) There, Eq. 5 gives the standard chemical potential of a molecule in solution in terms of an integral that explicitly includes solvent degrees of freedom. It is a "standard" chemical potential in the sense that, instead of allowing an arbitrary system volume of V, it effectively integrates the motions of the solute molecule over a "standard volume" equal to the reciprocal of the standard concentration, Co. Eqs. 34-37 of the same paper then show how this chemical potential can be rewritten in an implicit solvent form, where the solvent integrals have not been discarded or approximated, but only mathemetically tucked inside the solvation free energy as a function of solute conformation. The form of this expression exactly matches what one would obtain for an ideal gas IF the solvent term were magically turned into part of the potential energy and thereby lost its temperature dependence. In this specific sense, then, the contribution of translation to the chemical potential of a molecule in solution is, indeed, the same as what one would obtain from an ideal gas model. It's maybe more immediately relevant to point out that the solvation free energy of the solute is equal to the difference between its standard chemical potential in solution vs gas phase, where we have to use the same standard concentration (e.g., 1 mol/liter) in both phases. When this difference is taken, the contribution of translation (i.e., the contribution of Co) cancels entirely, so that there is no translational contribution to the solvation free energy to worry about in the first place. Hence my opening comment. (Actually, this cancellation occurs for any concentration, so long as it is the same in both phases and ideality is assumed.) Note too, that, for a molecule at a given concentration in both solution and in gas phase, the spatial probability distribution function p(x) is the same in both phases. Therefore, if one (somewhat simplistically) writes the translational entropy as -R\int p(x)\ln p(x), one finds the translational entropies are equal in both phases. Indeed, although "solvent caging" certainly occurs in solution, it operates only a short time-scale; over the experimental time-frame, the solutes wander freely. So, although "caging" presumably is a factor in the solvation free energy, I would not say it contributes to a translational term. It should already be included in the model itself, perhaps via some kind of surface energy, scaled particle theory, etc. Regards, Mike From owner-chemistry@ccl.net Thu Dec 4 16:09:00 2008 From: "Mihaly Mezei Mihaly.Mezei!A!mssm.edu" To: CCL Subject: CCL: Cremer-pople parameters Message-Id: <-38251-081204102650-10341-c/bQH1w0iisW/OAe3pgUlQ _ 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: Thu, 04 Dec 2008 10:26:34 -0500 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei##mssm.edu] ----- Original Message ----- > From: "Neha Gandhi n.gandhiau[a]gmail.com" Date: Thursday, December 4, 2008 12:38 am Subject: CCL: Cremer-pople parameters > > Sent to CCL by: "Neha Gandhi" [n.gandhiau===gmail.com] > Hi, > > I am looking for a program which can help me to calculate Cremer-Pople > ring puckering parameters for pyranose or in general six member rings > > from the AMBER trajectories. I heard about Mark Foster's program > QCPE,but its hard to visualise. > > I am grateful for you reply, > > Regards, > Neha Gandhi, > School of Biomedical Sciences, > Curtin University of Technology, > GPO Box U1987 Perth, > Western Australia 6845 > > My program Simulaid can do that (http://inka.mssm.edu/~mezei/simulaid) Regards, > Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU 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 Thu Dec 4 23:57:00 2008 From: "vijayan_rs(_)iicb.res.in" To: CCL Subject: CCL: How to model insertions in proteins? Message-Id: <-38252-081204074307-970-L1U5r0UD2KXMMwXAru7CAQ a server.ccl.net> X-Original-From: vijayan_rs#%#iicb.res.in Content-Type: multipart/mixed; boundary="----=neXtPaRt_1228394406" Date: Thu, 4 Dec 2008 17:12:34 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: vijayan_rs[]iicb.res.in ------=neXtPaRt_1228394406 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi You can try out the homology module of insight II. Check if u have any corresponding coordinates in some loop databases and also in PDB for the loop region if u are sure that the region is an Beta sheet then u can try out Fugue based alignment. else u can go for rigrous energy minimization for the region in question keeping the rest as satic. in case if u are only interested in studying the active site and if u notic that the SVR(structurally variable region )is quite far away from the active side then u can proceed with docking or SBDD studies ------=neXtPaRt_1228394406 Content-Type: text/plain; mail scanned for viruses & found to be cleaned ------=neXtPaRt_1228394406--