Hi Tsjerk, Thanks for your suggestion.I tried to change the ions.itp as follows :
#ifdef _FF_AMBER03 [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1 #endif But still I am getting same problem.Kindly advice. Regards, Swati > Hi Swati, > > Sorry, I wasn't paying that much attention indeed and failed to > notice you were dealing with Amber. There's nothing wrong with your > installation in this regard; Gromacs just does not have Amber included > by default. I'm not sure if there's an ions.itp for Amber somewhere, > but it's not too hard writing the moleculetype 'Na' yourself. Just > take one of the ones in ions.itp and set the names and atom type > accordingly. > > Hope it helps, > > Tsjerk > > On Wed, Apr 22, 2009 at 10:14 AM, <swa...@ncbs.res.in> wrote: >> Hi Tsjerk, >> Thanks for your reply. ions.itp is already included in topology file. >> However after you mentioned I checked the ions.itp file. But I think it >> defines molecule type only for gromacs force fields and the OPLS force >> field. The headers are only these three >> #ifdef _FF_GROMACS >> #ifdef _FF_GROMOS96 >> #ifdef _FF_OPLS >> Is this a problem with my GROMACS installation? Kindly advice. >> Thanks. >> Swati >> >> >>> Hi Swati, >>> >>>> Fatal error: >>>> No such moleculetype Na >>>> >>>> But the atom type is present in ffamber03.rtp. I tried changing the >>>> atom >>>> name to NA and Na+. But I still get similar error. Kindly help. >>> >>> It doesn't complain about the atom type, but about the moleculetype. >>> Did you #include "ions.itp"? That file contains the moleculetype >>> definitions for a series of ions, including Na/NA/NA+. The naming >>> depends on the force field. >>> >>> Cheers, >>> >>> Tsjerk >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> Junior UD (post-doc) >>> Biomolecular NMR, Bijvoet Center >>> Utrecht University >>> Padualaan 8 >>> 3584 CH Utrecht >>> The Netherlands >>> P: +31-30-2539931 >>> F: +31-30-2537623 >>> _______________________________________________ >>> 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 gmx-users-requ...@gromacs.org. >>> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php