Have a look at the rtp file of the force field u r using for correct representation of the ion used..
With regards, J. John Wesly, FInal Year, B.Tech., Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India. <~WesFaith~> "He who desire to learn, pursues towards edification... One who has will to do, finds a way how to do. Have a LEARNING SPREE.... Desire to learn... Passion to know things... Unravel the mysteries about your abilities... " On Sun, Dec 26, 2010 at 12:26 PM, shikha agarwal <shikhaiiit...@gmail.com>wrote: > hello , > > this is my ions.itp file for gromos53a6 forcefield > > [ moleculetype ] > ; molname nrexcl > CU1 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CU1+ 1 CU1 CU 1 1 63.54600 > > [ moleculetype ] > ; molname nrexcl > CU 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CU2+ 1 CU CU 1 2 63.54600 > > [ moleculetype ] > ; molname nrexcl > ZN 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 ZN2+ 1 ZN ZN 1 2 65.37000 > this is my ions.itp > > [ moleculetype ] > ; molname nrexcl > MG 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 MG2+ 1 MG MG 1 2 24.30500 > > [ moleculetype ] > ; molname nrexcl > CA 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CA2+ 1 CA CA 1 2 40.08000 > > [ moleculetype ] > ; molname nrexcl > NA 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 NA+ 1 NA NA 1 1 22.9898 > > [ moleculetype ] > ; molname nrexcl > CL 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CL- 1 CL CL 1 -1 35.45300 > > > > > for adding ions I used this command ... > > genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 > -nname CL- > > now when I m doing EM then getting this error > > grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr > > Fatal error: > No such moleculetype NA+ > > > help me ! > > regards: > shikha > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists