Dear yang thanks very much.the some of atomes do not found(NR,CH,N5,...).they are in lipid.itp best wishes --- Yang Ye <[EMAIL PROTECTED]> wrote:
> You shall read up manual for the structure of > topology file. > > For your problem, you shall create a top file which > contains > > #include "ffgmx.itp" > #include "lipid.itp" > #include "popc.itp" > #include "prox.itp" > #ifdef POSRES > ; #include "prox-posre-100000.itp" > #include "prox-posre.itp" > #endif > #include "spc.itp" > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > ; Include generic topology for ions > #include "ions.itp" > [ system ] > ; Name > protein and POPC > [ molecules ] > ; Compound #mols > Protein_X 1 > POP 489 > > Regards, > Yang Ye > > ----- Original Message ---- > From: mahbubeh zarrabi <[EMAIL PROTECTED]> > To: Yang Ye <[EMAIL PROTECTED]>; Discussion list > for GROMACS users <gmx-users@gromacs.org> > Sent: Monday, May 28, 2007 7:56:23 PM > Subject: Re: [gmx-users] simulation popc > > > dear freind > thanks for helping. there is another errore: no such > moleculetype protein. > best wishes > --- Yang Ye <[EMAIL PROTECTED]> wrote: > > > Put two semicolon before > > > > ;[ defaults ] > > ;1 1 > > > > in the lipid.itp > > > > ----- Original Message ---- > > From: mahbubeh zarrabi <[EMAIL PROTECTED]> > > To: gmx-users@gromacs.org > > Sent: Monday, May 28, 2007 4:41:19 PM > > Subject: [gmx-users] simulation popc > > > > > > Dear all > > I want to simulate protein in popc.I dowanload > > popc128a.pdb from tieleman site and insert protein > > in > > popc by VMD BUT I can not run grompp.there is > > errore: > > found a second defaults directive file ffgmx.itp > > line6.whould you please help me?which protocole is > > useful for me(in detail)? > > best regard > > > > > > > > > > > ____________________________________________________________________________________ > > Bored stiff? Loosen up... > > Download and play hundreds of games for free on > > Yahoo! Games. > > http://games.yahoo.com/games/front > > _______________________________________________ > > 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 > > > > > > ____________________________________________________________________________________ > Need Mail bonding? > Go to the Yahoo! Mail Q&A for great tips from Yahoo! > Answers users. > http://answers.yahoo.com/dir/?link=list&sid=396546091> _______________________________________________ > 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 ____________________________________________________________________________________Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz _______________________________________________ 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