can i put the partial charges from Gaussian? --- 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
