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 [email protected] 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
