From owner-chemistry@ccl.net Fri Apr 18 03:14:01 2008 From: "alexandra.marques _ fc.up.pt" To: CCL Subject: CCL:G: fixing charges in gaussian input Message-Id: <-36780-080417204943-25721-IY0NyV7+o80CQH+/S8gyow~!~server.ccl.net> X-Original-From: alexandra.marques]![fc.up.pt Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Fri, 18 Apr 2008 01:48:52 +0200 MIME-Version: 1.0 Sent to CCL by: alexandra.marques#%#fc.up.pt Hi, I calculated ESP charges with Gaussian for a ligand. Now I want to use =20 them to fix charges for some atoms of a modified version of the =20 ligand. However I don=E2=80=99t know how to fix charges for some atoms in th= e =20 Gaussian input. Does anyone know how to do this? Regards, Alexandra ------------------------------------------------------------------------- A FCUP utiliza o sistema open source de webmail Horde/IMP (www.horde.org) Visite: http://www.fc.up.pt/ http://info.fc.up.pt/ From owner-chemistry@ccl.net Fri Apr 18 09:35:01 2008 From: "Chunhui Li baotogo2004^gmail.com" To: CCL Subject: CCL:G: Summary for Fe3+ complex calculation Message-Id: <-36781-080418093239-20407-A8EkbBD9/gMINN3xCPEd1g^^^server.ccl.net> X-Original-From: "Chunhui Li" Date: Fri, 18 Apr 2008 09:32:35 -0400 Sent to CCL by: "Chunhui Li" [baotogo2004{:}gmail.com] Hi, Some time ago I posted a question about Fe3+ complex calculation and there was a request for a summary. So here it is Many thanks to all of those that responded (see below). Your information is highly appreciated. Greetings, Lily ------------------------ Sent to CCL by: "Chunhui Li" [baotogo2004,gmail.com] Dear All, I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ (H2O)5 with an fluorocarbon which has an COO- end. The total size is about 30-40 atoms. I am using Spartan '06 window to find equilibrium geometry. my first question is to verify that my total charge is +2 and multiplicity is 6, is it right? Since the Fe3+ charge I got from optimization using UHF STO3G is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. my second question is: what method and basis set you think would be appropriate for this system? Will HF method work for just geometry optimization? I tried to use UHF 3-21G to optimize, but SCF failed to converge after 500 cycles. STO-3G did converge. My computer have 512M memory, do you think I need more memory for this calculation? another question is that I don't understand why 6-311G* and 6-311+G** don't work for this system. The output says Basis not supported for the above atom.( I assume it is not working for Fe, isn't it?) My last question is: which one is better, UHF or ROHF in this case? Thank you in advance! Lily ----------------------- Sent to CCL by: Pascal Boulet [pascal.boulet:univ-provence.fr] Dear Lily, Chunhui Li baotogo2004*gmail.com wrote: > Sent to CCL by: "Chunhui Li" [baotogo2004,gmail.com] > Dear All, > > I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ (H2O)5 with an fluorocarbon which has an COO- end. The total size is about 30-40 atoms. I am using Spartan '06 window to find equilibrium geometry. > > my first question is to verify that my total charge is +2 and multiplicity is 6, is it right? Since the Fe3+ charge I got from optimization using UHF STO3G is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. > There is of course a difference between formal charges (+3) and charges calculated using ab initio methods (+2.05). Roughly speaking, the difference between formal charges and ab initio charges reflects the difference between a totally ionic complex and the "true" complex. The formal charge for your molecule is +2, assuming that the formal charge on iron is +3. The fact that you obtain a +2.05 ab initio charge on Fe looks correct, although I would have expected an even lower charge (+1.6-1.8)! But I suppose this is a Mulliken charge, and Mulliken scheme tends to give too ionic charges. In addition, the basis set you use is far too small which prevents flexibility for a larger delocalisation of the electrons. Now for the multiplicity, if you are not sure, you should make "experiments" with various, appropriate mulitiplicities. > my second question is: what method and basis set you think would be appropriate for this system? Will HF method work for just geometry optimization? I tried to use UHF 3-21G to optimize, but SCF failed to converge after 500 cycles. STO-3G did converge. > In this case HF is a starting point for a calculation of better quality. You will need correlation energy for such a system, which is not accounted for in the HF method. If you cannot afford MP2 calculations, I would suggest a GGA-DFT method which is about the same computational effort as HF. > My computer have 512M memory, do you think I need more memory for this calculation? > See next answer on how to reduce the memory and reaching "better" quality. > another question is that I don't understand why 6-311G* and 6-311+G** don't work for this system. The output says Basis not supported for the above atom.( I assume it is not working for Fe, isn't it?) > Yes, probably. I don't know spartan, but is it possible to use "Effective Core Potentials" for core electrons? You would save time and memory, and you would get reliable results in combination with MP2 or DFT-GGA calculations. > My last question is: which one is better, UHF or ROHF in this case? > It really depends on what you are interested in! If you just want an optimized structure, I would start with ROHF first to same time (and eventually restart this calculation with UHF option to make sure you have a "good" geometry). But if you are interested in spin densities partition, of course, UHF calculation is compulsory. > Thank you in advance! > I hope this help. Pascal Dr. Pascal Boulet, Computational Chemist University of Provence Laboratoire Chimie Provence, UMR6264 Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet[A]univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet ---------------------------------------------------------- Sent to CCL by: Mariusz Radon [mariusz.radon-#-gmail.com] Dear Chunhui: > my first question is to verify that my total charge is +2 and > multiplicity is 6, is it right? As to multiplicity: for transition metal complexes you often cannot assign it in advance. In general, you should compare several cases. There is plenty of papers in this topic, see e.g. the names of Harvey and Pierloot. But for your case I would also expect the sextet to be the ground state. > Since the Fe3+ charge I got from optimization using UHF STO3G > is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. If you are using Mulliken or similar population analysis don't expect to reproduce the formal oxidation state (+3). However, look at the spin population of iron: it should be close to 5 unpaired electrons. > my second question is: what method and basis set you think would be > appropriate for this system? Will HF method work for just geometry > optimization? I tried to use UHF 3-21G to optimize, but SCF failed to > converge after 500 cycles. STO-3G did converge. STO-3G is definitely too small for iron for almost any quantitative considerations. I think you must use larger basis. > My last question is: which one is better, UHF or ROHF in this case? I think you should definitely use DFT, not HF for transition metal system! The question of appropriate functional is of course perrenial. But there is still the dillema whether to choose Resticted Open-Shell (RO-) or Unresticted (U-) version. As far as I know the majority of papers from transistion metal chemistry employ U-DFT formalism and it is sometimes claimed to work better, but I don't remember any paper systematically comparing both approaches. best regards, Mariusz Radon ----------------------------------- Send by Toomas Tamm Lily, I would not expect a Mulliken charge much above 2.0 on a Fe3+. For some titanium examples, see the attached paper. We have seen the same for other transition metals, too. I also recommend that you use more heavyweight software, such as Gaussian (or Turbomole - our own favourite - , or Dalton, or Molcas, etc) for transition metal calculations. These systems are tricky and just getting the SCF to converge may be non-trivial. It seems that you have already reached the limits of Spartan in terms of basis set availability, and the geometry optimizer appears to have trouble, too. For publication-quality results, using some form of electron correlation treatment (at least DFT, and then the choice of functional is another question, B3LYP may not be the best choice for a Fe-containing system) is of order. My answer to the UHF/ROHF question would be "it depends". What is the purpose of your calculation? What are the results to be compared to? In general, computational chemistry of transition metal compounds is often a bumpy road and I recommend getting help from someone with experience in these matters. With best wishes, -- Toomas Tamm e-mail: tamm (at) yki.ttu.ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ ------------------------------------------- Send by dr. Marcel Swart No, RHF or UHF do not work properly for these systems. You will need a good DFT functional to be able to describe the spin states correctly. The best DFT functional for iron systems is OPBE (OPTX + PBEc). GTO basis sets (like STO-3G, 6-31G* etc) have a problem with high spin states; it is better to use the Ahlrichs basis sets, but even they suffer from this problem. The total charge is indeed +2 (+3 from iron, -1 from FCH2COO-), and indeed multiplicity can be 6 (high spin), if it equal to the FE(H2O)6, but because of COO- ligand, this may change to a doublet (mult=2), or quartet (mult=4). Again, to be able to calculate this correctly, you will probably need a very large GTO basis set (or the STO basis sets of ADF). On Apr 10, 2008, at 9:48 PM, Chunhui Li baotogo2004*gmail.com wrote: Sent to CCL by: "Chunhui Li" [baotogo2004,gmail.com] Dear All, I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ (H2O)5 with an fluorocarbon which has an COO- end. The total size is about 30-40 atoms. I am using Spartan '06 window to find equilibrium geometry. my first question is to verify that my total charge is +2 and multiplicity is 6, is it right? Since the Fe3+ charge I got from optimization using UHF STO3G is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. my second question is: what method and basis set you think would be appropriate for this system? Will HF method work for just geometry optimization? I tried to use UHF 3-21G to optimize, but SCF failed to converge after 500 cycles. STO-3G did converge. My computer have 512M memory, do you think I need more memory for this calculation? another question is that I don't understand why 6-311G* and 6-311+G** don't work for this system. The output says Basis not supported for the above atom.( I assume it is not working for Fe, isn't it?) My last question is: which one is better, UHF or ROHF in this case? Thank you in advance! Lily =================================== dr. Marcel Swart ICREA researcher at Institut de Qumica Computacional Universitat de Girona Parc Cientfic i Tecnolgic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) -------------------------------------------------------------- Sent to CCL by: Mikael Johansson [mpjohans^^^chem.au.dk] Hello Lily and All! Chunhui Li baotogo2004*gmail.com wrote: I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ (H2O)5 with an fluorocarbon which has an COO- end. Just adding a bit to the quite complete answers by Pascal and Mariusz. I fully agree that DFT is the method of choice here, although it will have problems in conclusively deciding the correct spin state. It will probably give better results than MP2, too. B3LYP has of course been used extensively, but perhaps an even better choice would be BP86. It's non-hybrid, so depending on your program it can speed up calculations significantly. It might even get you a better geometry than B3LYP, see: Ryde and Nilsson, Quantum chemistry can locally improve protein crystal structures", JACS 125 (2003) 14232. Also, use UHF instead of ROHF. TM systems exhibit a lot of spin polarisation, which a restricted formalism naturally cannot capture. I'm not aware of a DFT ROKS comparison, but for nice colour pictures on the complete failure of Hartree-Fock at both UHF and ROHF levels for another iron complex (haem), I modestly suggest page 40 of my thesis: http://www.iki.fi/~mpjohans/science/thesis-summary-2007.pdf And yes, using ridiculously small basis sets will give you results of equal hilarity. Have a good weekend, Mikael J. http://www.iki.fi/~mpjohans From owner-chemistry@ccl.net Fri Apr 18 12:02:01 2008 From: "Gilles Frapper gilles.frapper*_*univ-poitiers.fr" To: CCL Subject: CCL: post-doc in France (Poitiers) Message-Id: <-36782-080418110639-21607-ABM7AaeGMA8f1nr7GIp0QQ]|[server.ccl.net> X-Original-From: Gilles Frapper Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 18 Apr 2008 16:14:50 +0200 MIME-Version: 1.0 Sent to CCL by: Gilles Frapper [gilles.frapper ~ univ-poitiers.fr] Dear Colleagues, Find enclosed a job advertisment for 1-year assistant professor position in our group in Poitiers (France) ; (poste ATER sept. 2008, 2300 €/month ; 192h/year teaching bachelor/master). As the candidate must speak fluently french, the announcement is in french ;-) Dateline : *april 23 !* Best regards -- Gilles Frapper, enseignant-chercheur Groupe de Chimie Quantique Appliquée LACCO UMR 6503 CNRS - Université de Poitiers 40 av.recteur Pineau 86022 Poitiers Cedex tél : 05 49 45 35 74 - fax : 05 49 4540 20 http://yargla.labo.univ-poitiers.fr / gilles.frapper|univ-poitiers.fr ------------------------------------------------------------------------------------------------------------------------------------------------------ Poste d'ATER pour la rentrée 2008 à l'université de Poitiers en section 31 CNU profil : *CHIMIE THEORIQUE APPLIQUEE A LA CATALYSE HETEROGENE* Un poste d'ATER sera ouvert au concours au printemps 2008 au titre de l'année universitaire 2008-2009. Un poste de Maître de Conférences avec le même profil doit être ouvert lors de la campagne de recrutement 2009. Le ou la candidat-e devra posséder un doctorat en chimie théorique. Un dossier doit être déposé impérativement à l'université de Poitiers pour la campagne de recrutement 2008 (avant la publication des profils de postes !). Il ou elle intégrera le groupe de chimie quantique appliquée du laboratoire de catalyse en chimie organique (UMR 6503 CNRS). http://labo.univ-poitiers.fr/umr6503/ Descriptif recherche: - Chimie quantique appliquées aux systèmes périodiques et moléculaires. - Modélisation d'interfaces solide-gaz, solide-liquide [ex. nanotubes de carbone,zéolithes, surfaces métalliques, ...]. - Compétences souhaitées : *connaissances des méthodes DFT, ab initio, QM/MM. *dynamique moléculaire. *gestion des systèmes informatiques et des programmes. Descriptif enseignement (niveaux L&M) : Chimie théorique & modélisation Chimie générale Informatique appliquée à la chimie Contact (par courriel de préférence) : Gilles Frapper gilles.frapper|univ-poitiers.fr 05 49 45 35 74 Groupe Chimie Quantique Appliquée - http://yargla.labo.univ-poitiers.fr/ LACCO UMR 6503 CNRS 40, av. du recteur Pineau 86022 Poitiers Cedex ----------------------- Inscription en ligne jusqu'au 23 avril : https://puppis.scx.univ-poitiers.fr/bin/WebObjects/RecrutATER http://www.univ-poitiers.fr/jsp/fiche_pagelibre.jsp?CODE=40723646&LANGUE=0&RH=1203156725980&RF=1185287478244 From owner-chemistry@ccl.net Fri Apr 18 17:39:01 2008 From: "mmooney05**qub.ac.uk" To: CCL Subject: CCL: Grid Centre Autodock4 Message-Id: <-36783-080418085942-17255-ZDRgxfoWN6hCff7mniSEug|-|server.ccl.net> X-Original-From: mmooney05/./qub.ac.uk Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 18 Apr 2008 12:41:05 +0100 Mime-Version: 1.0 Sent to CCL by: mmooney05!A!qub.ac.uk Hi all, I have a question regarding the analysis of .dlg files in Autodock4.= =20 I have found a solution to the problem, but don=92t know how to carry it ou= t.=20 I would like to know how to shift/translate the receptor molecule according= =20 to the value of the grid centre, specified in the .gpf file. This problem= =20 has caused my docked ligand to sit too far away from the receptor, thus it= =20 doesn=92t appear to be docked. I would most appreciate some advice or suggestions regarding this issue. Many Thanx, Maura From owner-chemistry@ccl.net Fri Apr 18 18:14:01 2008 From: "Nancy A Neale nealen#%#mail.nih.gov" To: CCL Subject: CCL:G: UV-Vis spectra prediction Message-Id: <-36784-080418084059-15387-Tixf4Kam84fPqpXBXzr6kg(-)server.ccl.net> X-Original-From: "Nancy A Neale" Date: Fri, 18 Apr 2008 08:40:55 -0400 Sent to CCL by: "Nancy A Neale" [nealen:_:mail.nih.gov] Dear David Gallagher, I am interested in this subject area as well. Please, may I also have a copy of your presentation? Thank you, Nancy Neale email: nneale[#]mail.nih.gov > "Sue Lam chsue2004#yahoo.com" wrote: > > Sent to CCL by: Sue Lam [chsue2004|-|yahoo.com] > --0-2006443586-1208406809=:8689 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear David Gallagher, > > I am also interested in that topic. Could I have a copy of your powerpoint? > > Thanks, > Sue > > "David Gallagher gallagher.da{=}gmail.com" wrote: > Bonjour Jerome, > > The band-width is related to the gradient of the excited state at the transition, i.e. a high gradient allows access to more vibrational levels > from the ground state and hence, a higher band-width, conversely a low gradient gives a narrow peak. I have some Powerpoint slides on UV-spectra that I put together a few years ago explaining the concept . Please let me know if you want a copy of them. > > Regards, > David Gallagher > CACheResearch.com > > At 05:16 AM 4/16/2008, Jerome Kieffer Jerome.Kieffer{=}terre-adelie.org wrote: > Dear CCLers, > > I am trying to reproduce experimental UV-spectra of organic molecules : > > After the conversion wavelength (nm) -> energy (cm-1) of the experimental spectrum, I deconvoluted it by a sum of gaussian functions (using FitYK). It fits well. > > Transitions I obtained using TDDFT are pretty good compared with the center of the gaussian deconvolution, but the FWHM of the experimental spectrum's gaussian varies from 2000 to 8000 cm-1. > > So my question is: is it possible to calculate the broadening of an absorption band ? some software like gausssum suggest a FWMH of arround 3000cm-1 > Thank you for your help > > Regards > > --------------------------------- > Jrme Kieffer > http://www.terre-adelie.org > > > --------------------------------- > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. > --0-2006443586-1208406809=:8689 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear David Gallagher,
 
I am also interested in that topic. Could I have a copy of your powerpoint?
 
Thanks,
Sue

"David Gallagher gallagher.da{=}gmail.com" <owner-chemistry,ccl.net> wrote:
Bonjour Jerome,

The band-width is related to the gradient of the excited state at the transition, i.e. a high gradient allows access to more vibrational levels > from the ground state and hence, a higher band-width, conversely a low gradient gives a narrow peak.  I have some Powerpoint slides on UV-spectra that I put together a few years ago explaining the concept . Please let me know if you want a copy of them.

Regards,
David Gallagher
CACheResearch.com

At 05:16 AM 4/16/2008, Jerome Kieffer Jerome.Kieffer{=}terre-adelie.org wrote:
>
Dear CCLers,

I am trying to reproduce experimental UV-spectra of organic molecules :

After the conversion wavelength (nm) ->  energy (cm-1)  of the experimental spectrum,  I deconvoluted it by a sum of gaussian functions (using FitYK). It fits well.

Transitions I obtained using TDDFT are pretty good compared with the center of the gaussian deconvolution,  but the FWHM of the experimental spectrum's gaussian varies from 2000 to 8000 cm-1.

So my question is: is it possible to calculate the broadening of an absorption band ? some software like gausssum suggest a FWMH of arround 3000cm-1   
Thank you for your help

Regards
Jrme Kieffer
http://www.terre-adelie.org

> >

Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > --0-2006443586-1208406809=:8689-- > > From owner-chemistry@ccl.net Fri Apr 18 18:49:00 2008 From: "Maura Catherine Mooney mmooney05,+,qub.ac.uk" To: CCL Subject: CCL: Grid Centre in Autodock4 Message-Id: <-36785-080418080507-11971-DWLsPtb1Z25c6hamFD7Nsw],[server.ccl.net> X-Original-From: "Maura Catherine Mooney" Date: Fri, 18 Apr 2008 08:05:02 -0400 Sent to CCL by: "Maura Catherine Mooney" [mmooney05:+:qub.ac.uk] Hi all, I have a question regarding the analysis of .dlg files in Autodock4. I have found a solution to the problem, but dont know how to carry it out. I would like to know how to shift/translate the receptor molecule according to the value of the grid centre, specified in the .gpf file. This problem has caused my docked ligand to sit too far away from the receptor, thus it doesnt appear to be docked. I would most appreciate some advice or suggestions regarding this issue. Many Thanx, Maura From owner-chemistry@ccl.net Fri Apr 18 19:25:00 2008 From: "David Gallagher gallagher.da{}gmail.com" To: CCL Subject: CCL:G: [CCL]:G: UV-Vis spectra prediction Message-Id: <-36786-080418190523-9405-joc6O4FfksehdL8CWzcl7w{}server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 18 Apr 2008 16:05:07 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da/./gmail.com] Hi Nancy, The presentation is now on the web at http://www.cacheresearch.com/presentations.html , so please help yourself. If you have any problems with the download or any questions, then feel free to contact me again. Regards, David Gallagher CACheResearch.com At 05:40 AM 4/18/2008, Nancy A Neale nealen#%#mail.nih.gov wrote: >Sent to CCL by: "Nancy A Neale" [nealen:_:mail.nih.gov] >Dear David Gallagher, > >I am interested in this subject area as well. Please, may I also >have a copy of your presentation? > >Thank you, > >Nancy Neale >email: nneale-.-mail.nih.gov > > > "Sue Lam chsue2004#yahoo.com" wrote: > > > > Sent to CCL by: Sue Lam [chsue2004|-|yahoo.com] > > --0-2006443586-1208406809=:8689 > > Content-Type: text/plain; charset=iso-8859-1 > > Content-Transfer-Encoding: 8bit > > > > Dear David Gallagher, > > > > I am also interested in that topic. Could I have a copy of your > powerpoint? > > > > Thanks, > > Sue > > > > "David Gallagher gallagher.da{=}gmail.com" wrote: > > Bonjour Jerome, > > > > The band-width is related to the gradient of the excited state at > the transition, i.e. a high gradient allows access to more > vibrational levels > from the ground state and hence, a higher > band-width, conversely a low gradient gives a narrow peak. I have > some Powerpoint slides on UV-spectra that I put together a few > years ago explaining the concept . Please let me know if you want a > copy of them. > > > > Regards, > > David Gallagher > > CACheResearch.com > > > > At 05:16 AM 4/16/2008, Jerome Kieffer > Jerome.Kieffer{=}terre-adelie.org wrote: > > Dear CCLers, > > > > I am trying to reproduce experimental UV-spectra of organic molecules : > > > > After the conversion wavelength (nm) -> energy (cm-1) of the > experimental spectrum, I deconvoluted it by a sum of gaussian > functions (using FitYK). It fits well. > > > > Transitions I obtained using TDDFT are pretty good compared with > the center of the gaussian deconvolution, but the FWHM of the > experimental spectrum's gaussian varies from 2000 to 8000 cm-1. > > > > So my question is: is it possible to calculate the broadening of > an absorption band ? some software like gausssum suggest a FWMH of > arround 3000cm-1 > > Thank you for your help > > > > Regards > > > > --------------------------------- > > Jrme Kieffer > > http://www.terre-adelie.org > > > > From owner-chemistry@ccl.net Fri Apr 18 22:51:00 2008 From: "chana]|[marionegri.it" To: CCL Subject: CCL: Grid Centre Autodock4 Message-Id: <-36787-080418195949-14537-1wCKvmSnU7tlag1c+f4wEQ{=}server.ccl.net> X-Original-From: chana*_*marionegri.it Content-disposition: inline Content-transfer-encoding: quoted-printable Content-type: text/plain; format=flowed; DelSp=Yes; charset=ISO-8859-1 Date: Sat, 19 Apr 2008 01:35:39 +0200 MIME-version: 1.0 Sent to CCL by: chana-,-marionegri.it Dear Maura, I have found the same problem. I guess is a bug, the output maps are =20 shifted from the indicated coordinates although everything seems to be =20 correct in the gpf file. You can check it if you show the grids after =20 running autogrid in ADT; there you will see that the maps are shifted =20 > from the position you indicated and therefore ligand is docked exactly =20 where the software says, yet not in the place you intended so. I have solved this problem setting the coordinates of the whole system =20 placing the centre of the binding pocket to 0.0 0.0 0.0 and it works. =20 I also set the mass centre of the ligand to the same position, but I =20 reckon this would not be necessary. I guess the bug must consist in =20 symmetry operation running wild at some point, so better in that way. Best regards, Antonio Quoting "mmooney05**qub.ac.uk" : > > Sent to CCL by: mmooney05!A!qub.ac.uk > Hi all, > I have a question regarding the analysis of .dlg files in =20 > Autodock4. I have found a solution to the problem, but don=92t know =20 > how to carry it out. I would like to know how to shift/translate the =20 > receptor molecule according to the value of the grid centre, =20 > specified in the .gpf file. This problem has caused my docked ligand =20 > to sit too far away from the receptor, thus it doesn=92t appear to be =20 > docked. > > I would most appreciate some advice or suggestions regarding this issue. > > Many Thanx, > Maura > > > > -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/