I wanted the OPLS-UA because my system is large (3 proteins with 2 organic molecules, in water), and, if the G43a1 forcefield gives me a MD speed of 70 ps/day, an all atom model will result much slower. So what else can I do to speed up my MD, to get results in 1-3 months?. Mensaje citado por David van der Spoel <sp...@xray.bmc.uu.se>:
> Lucio Ricardo Montero Valenzuela wrote: > > So it 's better to switch to the OPLS forcefield if I want to compute the > > charges?. > > How can I implement the OPLS-UA if my gromacs (version 3.3) only includes > the > > OPLS-AA? > > We don't support United atom OPLS because Jorgensen himself does not use > it anymore. That if something should indicate for you that the united > atom force field has been superseded by the all-atom. Jorgensen himself > uses OPLS-AA with TIP4P, so this is probably the best recommendation. > Most important, if you chose to use another combination, you basically > have to prove that this "works" as well (whatever that means...) > > > Mensaje citado por "Justin A. Lemkul" <jalem...@vt.edu>: > > > >> > >> Lucio Montero wrote: > >>> How about MOPAC to calculate the charges for 3-methyladenine (this > >>> molecule has a charge +1) for using the G43a1 force field?. > >>> > >>> > >> That may not be a bad place to start, but any parameters applied to a > Gromos > >> molecule have to reproduce condensed phase thermodynamic observables. > >> Empirical > >> fitting of the initial parameters may be required. Refer to the primary > >> literature. The reference for the 53a5 and 53a6 parameter sets are > published > >> in > >> JCC, which may provide you with some useful information. > >> > >> -Justin > >> > >>> -------------------------------------------------- > >>> From: "Ran Friedman, Biochemisches Inst." <r.fried...@bioc.uzh.ch> > >>> Sent: Friday, March 27, 2009 2:35 PM > >>> To: <bije...@yahoo.com.br>; "Discussion list for GROMACS users" > >>> <gmx-users@gromacs.org> > >>> Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace > >>> PRODRGassignedones > >>> > >>>> Dear Josmar, > >>>> > >>>> You haven't written which force field you plan to use. For OPLS and > >>>> AMBER QM-based optimisation should be fine. In Gromos, the FF was > >>>> developed with the aim of reproducing experimental results and I'm not > >>>> sure if you can find a better solution than examining other residues > >>>> with the same chemical moieties or use the same approach as reported > >>>> in the relevant manuscripts. Some software packages can also be used - > >>>> these are mostly proprietary and not so easy to use. > >>>> > >>>> Once you derive the parameters, it's a good idea to make some test > >>>> runs of the ligands and see if they behave as expected before you > >>>> actually run a simulation with the protein. For example, if a > >>>> conjugate ring system isn't planar something may be wrong in the > setting. > >>>> > >>>> There's no easy solution - this is why it's considered an advanced > >>>> topic. It is, however, very important. I've encountered a ligand that > >>>> leaves its binding site during a simulation due to wrong parameters > >>>> (in this case, the protonation of a protein side chain - FEBS 581, > >>>> Pages 4120-4124, 2007). > >>>> > >>>> Hope that helped, > >>>> Ran > >>>> > >>>> On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) > >>>> "Josmar R. da Rocha" <bije...@yahoo.com.br> wrote: > >>>>> Dear users, > >>>>> > >>>>> I have been reading some posts about using externally computed > >>>>> charges to replace Prodrg charges at ligand topology files. Many > >>>>> users commented on the low trustability given to Prodrg charges (e.g > >>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; > >>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). > >>>>> Dr. Verli pointed out the use of semi-empirical methods such as RM1 > >>>>> in cases not involving simulations with sulphate or phosphate groups > >>>>> (what is not my case) and the use of QM methods with the 6-31G** > >>>>> basis set, for example, to obtain robust charges > >>>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On > >>>>> the other hand Dr. Mobley defined as a "a bad idea to compute charges > >>>>> for an all-atom case using QM and then try to convert these to a > >>>>> united atom force field". Other users advice that the best charges > >>>>> are that compatible with the force field parametrization > >>>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; > >>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), > >>>>> usually pointing to > >>>>> http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman > >>>>> suggested that "to calculate the electrostatic potential over the > >>>>> whole molecule, and fit the atomic charges so that they reproduce > >>>>> this potential" in order to make it less sensitive to small changes > >>>>> in the geometry of the molecule may give good results > >>>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). > >>>>> Dr. Lemkul stressed the need for charges refinement to reproduce > >>>>> experimentally-observed behavior while trying to use QM charges with > >>>>> Gromos ff. since "Parameterization under Gromos usually involves > >>>>> empirical derivation of physical parameters, and free energy > >>>>> calculations using thermodynamic integration". Few examples of > >>>>> protein-ligand studies using Gromacs and Gromos96 ff that I have > >>>>> access (from literature) seem to treat it as "take it for granted" > >>>>> issue (any reference with a more detailed description would be > >>>>> welcome :-)). Despite reading on this topic I could not compile all > >>>>> the information in a clear and objective way (may be because I'm in > >>>>> the wrong track). Let ask you some question that I find would help me > >>>>> to make my ideas more clear: > >>>>> > >>>>> > >>>>> 1-am I overestimating the importance of ligand charges in such a > >>>>> simple study of protein-small molecule (containg charged Phosphate > >>>>> groups) complex? or > >>>>> > >>>>> 1.1-The only way to test for this is doing many different simulation > >>>>> on the same system using different type of computed charges to see > >>>>> what happen? > >>>>> > >>>>> 2-How could I try to choose a method to obtain reasonable charges > >>>>> based on the reproduction of experimentally-observed behavior if I do > >>>>> not have experimental data for my system? > >>>>> > >>>>> 3-I also would like to know from users dealing with protein-ligand > >>>>> interactions studies what do you consider a good approach to address > >>>>> this problem? > >>>>> > >>>>> Based on what I read I'd have a tendency to use HF/6-31G** ESP > >>>>> derived charges (with necessary changes as to make it united-atom > >>>>> charges and scaling that to a integer number for each group). Please, > >>>>> let me know if that strategy would be as good as a disaster! Thank > >>>>> you very much for the attention. > >>>>> > >>>>> > >>>>> Josmar Rocha > >>>>> > >>>>> > >>>>> > >>>>> Veja quais são os assuntos do momento no Yahoo! +Buscados > >>>>> http://br.maisbuscados.yahoo.com > >>>> > >>>> > >>>> _______________________________________________ > >>>> gmx-users mailing list gmx-users@gromacs.org > >>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>> Please search the archive at http://www.gromacs.org/search before > >>>> posting! > >>>> Please don't post (un)subscribe requests to the list. Use the www > >>>> interface or send it to gmx-users-requ...@gromacs.org. > >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> _______________________________________________ > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>> Please search the archive at http://www.gromacs.org/search before > posting! > >>> Please don't post (un)subscribe requests to the list. Use the www > >>> interface or send it to gmx-users-requ...@gromacs.org. > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >> -- > >> ======================================== > >> > >> Justin A. Lemkul > >> Graduate Research Assistant > >> ICTAS Doctoral Scholar > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> ======================================== > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > Lucio Ricardo Montero Valenzuela > > Instituto de Biotecnologia, UNAM > > Departamento de Biologia Molecular de Plantas > > Av. Universidad 2001, Col. Chamilpa > > Cuernavaca 62210 > > Mexico > > > > ---------------------------------------------------------------- > > Este mensaje fue enviado desde el servidor Webmail del Instituto de > Biotecnologia. > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico ---------------------------------------------------------------- Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
