Hi Berk and all, one more question: When dealing with dummy atoms in mutations using oplsaa FF, we cannot simply mutate the atomtype but still need to find and provide exact parameters for the bonds, angles, etc. (ohterwise, there is error " No default bond types") AM I right?
Or there is some automatic way in gromacs? thanks a lot Li Qiang On Fri, Nov 21, 2008 at 6:03 PM, Berk Hess <[EMAIL PROTECTED]> wrote: > Yes. > > Gromos96 is the "inconvenient" force field in this respect (not OPLS). > In all other common biomolecular force fields you only need to change > the atom types, charges and masses. > > Berk > > > Date: Fri, 21 Nov 2008 18:01:15 +0800 > > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] OPLSAA parameters > > > > I mean in mutation free energy calculations. > > > > for OPLSAA force field we only need to provide the mutated atom types, > > but not need to change the [bonds], [angle] ...etc. in the topology file? > > Since in Gromos96, the parameters need to be provided for state B. > > > > thank you > > > > Qiang > > > > > > Berk Hess wrote: > > > Hi, > > > > > > Although optionally having the parameters in the top file > > > might be useful, for mutation studies you don't need this, > > > since you only need to change the atom types, > > > you never have to give the parameters explicitly. > > > > > > Berk > > > > > > > Date: Fri, 21 Nov 2008 16:10:06 +0800 > > > > From: [EMAIL PROTECTED] > > > > To: gmx-users@gromacs.org > > > > Subject: Re: [gmx-users] OPLSAA parameters > > > > > > > > Thanks Mark. > > > > > > > > Hope the developers can consider to output the parameters into .top > > > file > > > > explicitly. That would be helpful for mutation calculations at least, > I > > > > think. > > > > > > > > > > > > > > > > > > > > Mark Abraham wrote: > > > > > friendli wrote: > > > > >> Hi Mark, > > > > >> > > > > >> the atom types in .top file is opls_???, but the atom types(or > > > > >> "name") in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, > etc. > > > > >> > > > > >> So we still need to look up ffoplsaanb.itp to link these two "atom > > > > >> type" (or "name"), right? > > > > > > > > > > OK, whatever... as I said, different force fields have different > > > > > mechanisms. > > > > > > > > > > Mark > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > ------------------------------------------------------------------------ > > > Express yourself instantly with MSN Messenger! MSN Messenger > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > _______________________________________________ > > 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 > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > 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 >
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