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Yes.<br><br>Gromos96 is the "inconvenient" force field in this respect (not OPLS).<br>In all other common biomolecular force fields you only need to change<br>the atom types, charges and masses.<br><br>Berk<br><br>> Date: Fri, 21 Nov 2008 18:01:15 +0800<br>> From: friendli2000@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] OPLSAA parameters<br>> <br>> I mean in mutation free energy calculations.<br>> <br>> for OPLSAA force field we only need to provide the mutated atom types, <br>> but not need to change the [bonds], [angle] ...etc. in the topology file?<br>> Since in Gromos96, the parameters need to be provided for state B.<br>> <br>> thank you<br>> <br>> Qiang<br>> <br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> ><br>> > Although optionally having the parameters in the top file<br>> > might be useful, for mutation studies you don't need this,<br>> > since you only need to change the atom types,<br>> > you never have to give the parameters explicitly.<br>> ><br>> > Berk<br>> ><br>> > > Date: Fri, 21 Nov 2008 16:10:06 +0800<br>> > > From: friendli2000@gmail.com<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] OPLSAA parameters<br>> > ><br>> > > Thanks Mark.<br>> > ><br>> > > Hope the developers can consider to output the parameters into .top <br>> > file<br>> > > explicitly. That would be helpful for mutation calculations at least, I<br>> > > think.<br>> > ><br>> > ><br>> > ><br>> > ><br>> > > Mark Abraham wrote:<br>> > > > friendli wrote:<br>> > > >> Hi Mark,<br>> > > >><br>> > > >> the atom types in .top file is opls_???, but the atom types(or<br>> > > >> "name") in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, etc.<br>> > > >><br>> > > >> So we still need to look up ffoplsaanb.itp to link these two "atom<br>> > > >> type" (or "name"), right?<br>> > > ><br>> > > > OK, whatever... as I said, different force fields have different<br>> > > > mechanisms.<br>> > > ><br>> > > > Mark<br>> > > > _______________________________________________<br>> > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > > Please search the archive at http://www.gromacs.org/search before<br>> > > > posting!<br>> > > > Please don't post (un)subscribe requests to the list. Use the www<br>> > > > interface or send it to gmx-users-request@gromacs.org.<br>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > ><br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> > ------------------------------------------------------------------------<br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > ------------------------------------------------------------------------<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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