On Tue, Jun 17, 2008 at 02:21:09PM +0200, Xavier Periole wrote: > On Tue, 17 Jun 2008 17:31:53 +0530 (IST) > ANINDITA GAYEN <[EMAIL PROTECTED]> wrote: > > > > > >can i put the partial charges from Gaussian? > In principle you can do everything assuming that it is justified. > > Putting charges from Gaussian do not mean much. It sounds very elaborated > because Gaussian could imply that you include "ab initio" calculations. > However Gaussian also include semi-empirical methods! > > All that to say that the manner the charges are extracted from Gaussian > is much more relevant to be able to judge their quality.
although i would probably go for a b3lyp approach or so, semi-empirally-derived charges are not necessarily a bad thing, especially when a solvent reaction field was used. in any case they're a million times better than mulliken. > What you have to do is to convince yourself that the way you do is the > accurate enough to the application you like. > > In a general manner the RESP (see Amber web site) approach has shown > to be relative reliable. agreed. cheers, marc > >--- On Tue, 17/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > >>From: Justin A. Lemkul <[EMAIL PROTECTED]> > >>Subject: Re: [gmx-users] gromos parameterisation in OPLS > >>To: [EMAIL PROTECTED], "Gromacs Users' List" > >><gmx-users@gromacs.org> > >>Date: Tuesday, 17 June, 2008, 4:00 PM > >>If you include in the .itp file all the necessary > >>combinations in those > >>sections, then yes, the .itp file is reasonable and will > >>use the OPLS-AA > >>parameters for those specified items. Take care to get the > >>numbering > >>right after that point, because you will likely be > >>inserting lots of > >>hydrogens! > >> > >>-Justin > >> > >>ANINDITA GAYEN wrote: > >>> Sir, > >>> > >>> If i insert the hydrogen atoms in the first section of > >>the itp file, where atomnames , atomtypes , nr, cgnr are > >>displayed, wil it be wrong. Also, i was talking that, will > >>the inclusion of "ffoplsaa.itp" will serve the > >>bonded and nonbonded parameters if i supply the > >>connectivities in all the bonds, pairs, angles and dihedral > >>section by the atom numbers? > >>> > >>> Thanks for the requested answers. > >>> > >>> anindita > >>> > >>> > >>> > >>> > >>> --- On Mon, 16/6/08, Justin A. Lemkul > >><[EMAIL PROTECTED]> wrote: > >>> > >>> > >>>> From: Justin A. Lemkul <[EMAIL PROTECTED]> > >>>> Subject: Re: [gmx-users] gromos parameterisation > >>in OPLS > >>>> To: [EMAIL PROTECTED], "Discussion > >>list for GROMACS users" <gmx-users@gromacs.org> > >>>> Date: Monday, 16 June, 2008, 9:29 PM > >>>> Changing the atomtypes will only work if you have > >>explicit > >>>> inclusion of > >>>> all hydrogens in your PRODRG-generated topology. > >>Since the > >>>> PRODRG > >>>> server outputs a GROMOS-based .itp file, this is > >>unlikely > >>>> unless your > >>>> molecule contains only polar or aromatic groups. > >>If > >>>> we're still talking > >>>> about CHAPS or cholesterol, this will not be the > >>case. You > >>>> will have > >>>> nonpolar groups that, within GROMOS, are atomtype > >>CH1, CH2, > >>>> etc., but > >>>> OPLS will not have these UA representations. > >>>> > >>>> I'm not sure what you mean in the last > >>sentence. > >>>> Nothing in this > >>>> process will be automatically generated for you. > >>>> You're building your > >>>> topology by hand. Inclusion of > >>"ffoplsaa.itp" > >>>> will tell grompp which > >>>> parameters (bonded and nonbonded) apply to your > >>molecule. > >>>> Calling > >>>> "ffoplsaa.itp" will not tell any Gromacs > >>program > >>>> to automatically detect > >>>> and generate bonds, dihedrals, etc. > >>>> > >>>> The only way to have "automatic" > >>generation of > >>>> these parameters is to > >>>> build an .rtp entry for your molecule that > >>contains all of > >>>> this > >>>> information as well, and process your structure > >>with > >>>> pdb2gmx. This is > >>>> just as much work as building the topology > >>yourself, I > >>>> think. > >>>> > >>>> -Justin > >>>> > >>>> ANINDITA GAYEN wrote: > >>>> > >>>>> Hi, > >>>>> > >>>>> I came to know from the mailing list that if i > >>only > >>>>> > >>>> change the atomtype in the output itp file of > >>PRODRG2 and > >>>> put the charges as optimised by Gaussian; provided > >>i > >>>> include #include ffoplsaa.itp in the .top file of > >>the new > >>>> molecule and just keep the atom mumbers in > >>[bonds], > >>>> [pairs], [angles] and [dihedrals] as found in the > >>the all > >>>> atom pdb of PRODRG2, the resultant top file will > >>be a top > >>>> file in OPLS format. It was also stated there in > >>the > >>>> mailing list that for the atom numbers mentioned > >>the opls > >>>> staff will put the parameter values necccesary for > >>the > >>>> [bonds], [angles] etc. > >>>> > >>>>> Is the approach right? > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> From Chandigarh to Chennai - find > >>friends all > >>>>> > >>>> over India. Go to > >>>> http://in.promos.yahoo.com/groups/citygroups/ > >>>> > >>>>> > >>_______________________________________________ > >>>>> 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 > >>>>> > >>>> [EMAIL PROTECTED] > >>>> > >>>>> Can't post? Read > >>>>> > >>>> http://www.gromacs.org/mailing_lists/users.php > >>>> > >>>>> > >>>>> > >>>> -- > >>>> ======================================== > >>>> > >>>> Justin A. Lemkul > >>>> Graduate Research Assistant > >>>> Department of Biochemistry > >>>> Virginia Tech > >>>> Blacksburg, VA > >>>> jalemkul[at]vt.edu | (540) 231-9080 > >>>> > >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >>>> > >>>> ======================================== > >>>> > >>> > >>> > >>> Connect with friends all over the world. Get > >>Yahoo! India Messenger at > >>http://in.messenger.yahoo.com/?wm=n/ > >>> > >>> > >>> > >> > >>-- > >>======================================== > >> > >>Justin A. Lemkul > >>Graduate Research Assistant > >>Department of Biochemistry > >>Virginia Tech > >>Blacksburg, VA > >>jalemkul[at]vt.edu | (540) 231-9080 > >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >>======================================== > > > > > > Explore your hobbies and interests. Go to > >http://in.promos.yahoo.com/groups/ > > > >_______________________________________________ > >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 [EMAIL PROTECTED] > >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ----------------------------------------------------- > XAvier Periole - PhD > > NMR & Molecular Dynamics Group > University of Groningen > The Netherlands > http://md.chem.rug.nl/~periole > ----------------------------------------------------- > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- -- Marc F. Lensink Centre for Structural Biology and Bioinformatics CSBB Université Libre de Bruxelles [EMAIL PROTECTED] Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium tel: +32 2 650 5411 secr: +32 2 650 2013 fax: +32 2 650 5425 _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php