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Hi,<br><br>In 3 C and O are not atom names, but bonded atom types.<br>OPLS has non-bonded atom types opls_???<br>which in turn have bonded atom types.<br>There are far less bonded atom types then there<br>are non-bonded atom types.<br><br>Different force fields are set up in different ways.<br>OPLS is simple in some respects and more complex<br>in this respect (this is not a Gromacs but an OPLS issue).<br><br>Berk<br><br>> Date: Fri, 21 Nov 2008 14:32:25 +0800<br>> From: friendli2000@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] OPLSAA parameters<br>> <br>> <br>> So to obtain the parameters(e.g. bonds) in topology file,<br>> 1, read bond atoms in .top (e.g. 1 2)<br>> 2, find atom types of the bond atoms in .top (e.g. oplsaa_235, <br>> oplsaa_236)<br>> 3, find atom names of the above atom types in ffoplsaanb.itp (e.g. C, O)<br>> 4, check parameters in ffoplsaabon.itp<br>> <br>> Is that right? why it comes to such complex in GMX?<br>> <br>> thanks<br>> <br>> Qiang<br>> <br>> Mark Abraham wrote:<br>> > friendli wrote:<br>> >> In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type <br>> >> opls_235 and opls_236.<br>> >> While in oplsaanb.itp, the atom type opls_235 and opls_236 <br>> >> corresponds to atom "name"(as display in titles in oplsaanb.itp) C <br>> >> and O.<br>> >><br>> >> why there are two different "name"s for the same atom? what is the <br>> >> difference?<br>> ><br>> > Different force fields use the machinery differently, but I can't <br>> > think of a purpose for the atom name field in the parameter .itp file <br>> > if there is a separate atom type.<br>> ><br>> > The purpose of atom names, residue names and residue numbering in a <br>> > pre-pdb2gmx structure file is to look up the right atom types in the <br>> > .rtp file and write them to the .top file. The purpose of the atom <br>> > types in the .top file is to look up the right parameters in the .itp <br>> > file when running grompp. At that point, atom names are probably just <br>> > for user convenience.<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 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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