Yes, I used GROMOS87. Although it's deprecated now and I'm not sure which ff to switch to.
Hadas. On Sun, 2007-11-25 at 19:03 +0800, liang wrote: > Hi Hadas, > > i have tried to use gromos87 for protein, everything is ok. (just with > ffgmx.itp) > but if i use opls for protein, i have to add "ffoplsaa.itp" in top file, > otherwise it cannot provide some parameters for protein. > Did you use gromos87 to generate your protein itp files (chain_A .itp ...) ? > > Thanks > > Liang > > ----- Original Message ----- > From: "Hadas Leonov" <[EMAIL PROTECTED]> > To: "liang" <[EMAIL PROTECTED]>; "Discussion list for GROMACS users" > <[email protected]> > Sent: Sunday, November 25, 2007 5:26 PM > Subject: Re: [gmx-users] how to write the correct top file for > membraneprotein system? > > > > Hi Liang, > > > > Do you have to define ffoplsaa.itp in your top file? isn't it enough to > > generate your protein topology with the OPLS forcefield using pdb2gmx and > > include the protein's generated itp files? > > > > I don't use OPLS, but my own definition of the .top file goes like this: > > > > ; generic + lipid topology > > #include "ffgmx.itp" > > #include "lipid.itp" > > #include "dmpc.itp" > > #include "ions.itp" > > > > ; protein > > #include "chain_A.itp" > > #include "chain_B.itp" > > #include "chain_C.itp" > > #include "chain_D.itp" > > > > ; water > > #include "spc.itp" > > > > Rest of my molecule definitions are similar (protein first, then lipid, > > then > > water, and finally ions to neutralize the system). > > > > Hope it helps, > > Hadas. > > ----- Original Message ----- > > From: "liang" <[EMAIL PROTECTED]> > > To: "Justin A. Lemkul" <[EMAIL PROTECTED]> > > Cc: <[email protected]> > > Sent: Sunday, November 25, 2007 7:41 AM > > Subject: Re: [gmx-users] how to write the correct top file for > > membraneprotein system? > > > > > >> Dear Justin, > >> > >> Thanks for you quickly reply. > >> > >> I have tried before to comment out the section of [ defaults ] in the next > >> itp file, but still too many warnings and final crashed. > >> And i think it would not be the best method to solve this problem, because > >> i have to use ffgmx.itp to deal with DPPC. > >> > >> Is there any other method i can try? > >> > >> Thanks > >> > >> Liang > >> > >> ----- Original Message ----- > >> From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > >> To: "liang" <[EMAIL PROTECTED]>; "Discussion list for GROMACS > >> users" <[email protected]> > >> Sent: Sunday, November 25, 2007 12:23 PM > >> Subject: Re: [gmx-users] how to write the correct top file for membrane > >> protein system? > >> > >> > >>> Quoting liang <[EMAIL PROTECTED]>: > >>> > >>>> Dear User, > >>>> > >>>> i try to perform simulation on membrane protein ( proterin + DPPC ). > >>>> And i use OPLS for protein, Berger force field for DPPC. > >>>> But after i construct this system, i cannot obtain tpr file by using > >>>> grompp. > >>>> > >>>> Here is my topol.top : > >>>> > >>>> ; protein > >>>> #include "ffoplsaa.itp" > >>>> #include "protein-opls.itp" > >>>> > >>>> ; membrane > >>>> #include "ffgmx.itp" > >>>> #include "lipid.itp" > >>>> #include "dppc.itp" > >>>> > >>>> ; Include water topology > >>>> #include "spc.itp" > >>>> > >>>> [ system ] > >>>> ; name > >>>> Membrane in water > >>>> > >>>> [ molecules ] > >>>> ; name number > >>>> Protein 1 > >>>> DPPC 123 > >>>> SOL 14189 > >>>> > >>>> here is the result: > >>>> > >>> -------------------------------------------------------------------------------------------------------------------- > >>>> Fatal error: > >>>> Invalid order for directive defaults, file > >>>> ""/home/gmx331/share/gromacs/top/ffgmx.itp"", line 4 > >>>> > >>> -------------------------------------------------------------------------------------------------------------------- > >>> > >>> I suspect it is a result of using two different force fields. The [ > >>> defaults ] > >>> will be defined in the first force field (in your case, ffoplsaa.itp), > >>> but then > >>> grompp is finding a second [ defaults ] in ffgmx.itp. See here: > >>> > >>> http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file > >>> > >>> -Justin > >>> > >>>> > >>>> Could you please give me some suggestion? i appreciate your help. > >>>> > >>>> Thanks so much! > >>> > >>> > >>> > >>> ======================================== > >>> > >>> Justin A. Lemkul > >>> Graduate Research Assistant > >>> Department of Biochemistry > >>> Virginia Tech > >>> Blacksburg, VA > >>> [EMAIL PROTECTED] | (540) 231-9080 > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > >>> > >>> ======================================== > >>> > >> > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> 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 > >> > >> > >> > >> -- > >> No virus found in this incoming message. > >> Checked by AVG Free Edition. Version: 7.5.503 / Virus Database: > >> 269.16.5/1148 - Release Date: 11/23/2007 7:39 PM > >> > > > > _______________________________________________ gmx-users mailing list [email protected] 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
