Probably you generated a bad box. Check the box with i.e. rasmol and try to use -princ option in editconf (to put the protein in its inertial axes) and genion to make the ions to ensure charge neutrality. good luck, Adriana
> hi > today i have tried with some other protein but the problem still persists . > today i will tell you problem in detail > > today i have taken the protein pdb file which conatains only the amino > acids no hetero atoms > > i have run the pdb2gmx command > pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n > 1/out1.ndx -q 1/out1.pdb > > i got all the 5 files > > later i used the command edit conf > editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7 > > then i run the genbox > genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out 1.top > here i got the gro file and modified top file > > then i have run the grompp > grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr > my mdp file is > bellow > > ########################################################## > title = drg_trp > cpp = /usr/bin/cpp > define = -DFLEX_SPC > constraints = none > integrator = steep > dt = 0.002 ; ps ! > nsteps = 1000 > ns_type = grid > rlist = 0.9 > coulombtype = PME ; Use particle-mesh ewald > rcoulomb = 0.9 > rvdw = 1.0 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = le-5 > optimize_fft = yes > Tcoupl = no > Pcoupl = no > gen_vel = no > ; > ; Energy minimizing stuff > ; > emtol = 1000.0 > emstep = 0.01 > ############################################################### > There i got one NOTE : System has non-zero total charge: -6.999998e+00 > > later i tried to run the mdrun but the process fails at 24 steps > > Then i used the genion > > genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log > > here i got the modified gro file > but tere was warning that > turning of free energy, will use lambda=0 > Then i have edited the top file i got according to the gro file > since i m using the gromacs 3.3 the #include ions.itp was default > so i have removed the 7 water atoms from the top file and added 7 Na atoms > and run the grompp > > grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr > here the programme was failed showing the error > Fatal error: > No such moleculetype Na > i have checked the ions .itp > its having the information Na atom than why its showing this i could > n't understand > can any one help me over this here i have attatched my out6.gro file > and the top file > > Thanking you > Santosh Naik > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > -- _____________________________________________ Adriana Pietropaolo, PhD student, dipartimento di Chimica Fisica ed Inorganica, Facolta' di Chimica Industriale Universita' di Bologna WEB:www2.fci.unibo.it/~adriana Tel 051/6446992 FAX 051/2093690 _____________________________________________ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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