7/out7.gro is the out put of mdrun i have run for em
On 4/12/06, X.Periole <[EMAIL PROTECTED]> wrote: > > Your topology file does not correspond to the coordinate > file. You got to check both of them but the error is > certainly coming from the topology file. Not that you need > to include the ions.itp file after incerting the ions. > > It is better to insert the ions in the solvent Temp bath > and not in a separate bath. > > Your vdW cutoff is 1.0 nm. This is short if you do not do > it for a particular reason. > > You do not use indexes !! grompp does not complain about > non-defined groups ?? > > For the last grompp you run you give the 7/out7.gro as > starting configuration (-c option) which does not seem > to be the output of your em !! > > Solvating with genion is a new feature of GROMCAS ??? You > meant genbox probably. > > XAvier > > > hi guys > > i am working with the spider toxin protein and as > >mentioned early i > > was unable 2 over come this process > > > > below i have mentioning my problem in detail > > > > first i take the protein and run the pdb2 gmx command > >under the > > gromacs force field > > > > pdb2gmx -f spider.pdb -o 1/out1.gro -p 1/out1.top > > > > then i run the edit conf > > > > editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c > >-d 0.7 > > > > then i solvates the box using genion > > genion -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p > >1/out1.top > > > > then i run the grompp for energy minimisation > > using the em.mdp file given below > > > > title = drg_trp > > cpp = /usr/bin/cpp > > define = -DFLEX_SPC > > constraints = none > > integrator = steep > > dt = 0.002 ; ps ! > > nsteps = 500 > > nstlist = 10 > > 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 > > ; > > ; Energy minimizing stuff > > ; > > emtol = 1000.0 > > emstep = 0.01 > > > > > > grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o > >4/out4.tpr > > > > here i got one note > > NOTE: > > System has non-zero total charge: 2.000000e+00 > > > > then i used the genion command > > genion -s 4/out4.tpr -o 5/out5.gro -nname Cl -nn 2 -g > >5/out5.log > > > > now again i run the grompp > > now here i have edited the top file > > i removed 2 water molecule and added 2 cl molecules > > grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o > >6/out6.tpr > > > > then i have run the mdrun > > nohup mdrun -s 6/out6.tpr -o 7/out7.trr -c 7/out7.gro -g > >7/out7.log -e > > 7/out7.edr & > > > > then i tried to run the position restrained dynamic so i > >have tried with grompp > > > > using mdp file given below > > title = trp_drg > > warnings = 10 > > cpp = /lib/cpp ; location of cpp on SGI > > define = -DPOSRES > > constraints = all-bonds > > integrator = md > > dt = 0.002 ; ps ! > > nsteps = 10000 ; total 20.0 ps. > > nstcomm = 1 > > nstxout = 250 ; output coordinates every > >0.5 ps > > nstvout = 1000 ; output velocities every > >2.0 ps > > nstfout = 0 > > nstlog = 10 > > nstenergy = 10 > > nstlist = 10 > > ns_type = grid > > rlist = 0.9 > > coulombtype = PME > > rcoulomb = 0.9 > > rvdw = 1.0 > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 6 > > ewald_rtol = 1e-5 > > optimize_fft = yes > > ; Berendsen temperature coupling is on in four groups > > Tcoupl = berendsen > > tau_t = 0.1 0.1 0.1 0.1 > > tc_grps = protein IN4 sol Cl- > > ref_t = 300 300 300 300 > > ; Pressure coupling is on > > Pcoupl = berendsen > > pcoupltype = isotropic > > tau_p = 0.5 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; Generate velocites is on at 300 K. > > gen_vel = yes > > gen_temp = 300.0 > > gen_seed = 173529 > > > > grompp -f pr.mdp -c 7/out7.gro -p 1/out1.top -o > >8/out8.tpr > > > > here i got he error > > > >Fatal error: > > number of coordinates in coordinate file (7/out7.gro, > >7485) > > does not match topology (1/out1.top, 0) > > > > can any one help me over this issue > > > > 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 > > _______________________________________________ > 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 > _______________________________________________ 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
