Dear Justin Thank you very much My commands are: 1. add hydrogens, get top and gro files pdb2gmx -f 1z92.pdb -o 1z92.gro -p 1z92.top
2. specify the box size, and add water to the system editconf -f 1z92.gro -bt cubic -d 0.7 -o box.gro genbox -cp box.gro -cs spc216.gro -p 1z92.top -o sol.gro 3. grommpp -f em.mdp -p 1z92.top -c sol.gro -o em.tpr then found the system is charge -3 4. add 3NA+ ions in the SOL system genion -s em.tpr -p 1z92.tpr -p 1z92.top -o sol_ion.gro -pname NA+ -np 3 -nname CL- -nn 0 -random 5. perform the energy minimization simulation grompp -f em.mdp -p 1z92.top -o sol_ion.gro -o em.tpr mdrun -deffnm em -v Those commands until now then I should do position constraints and equil simulations with my pr.mdp and md.mdp parameters. I will check my .log file again to see if any errors occur Thank you very much Yi On 03/08/2009 15:56, "Justin A. Lemkul" <[email protected]> wrote: > > > houyi wrote: >> Dear all, >> I guess others have the same problem for me as well, and it may repeat >> to ask it again due to i am new for gromacs- 3.3.3. my protein is >> 1z92.pdb. when i perform the energy minimization , i got this error. but >> when i used for another small protein, which is 1ycr.pdb, it worked well >> for all. i choose the OPLS-AA/L all-atom force field >> my em.mdp is >> title = protein >> cpp = /usr/bin/cpp >> define = -DFLEX_SPC >> constraints = none >> integrator = steep >> dt = 0.002 ; ps ! >> nsteps = 100 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> rcoulomb = 1.0 >> rvdw = 1.0 >> ; >> ; Energy minimizing stuff >> ; >> emtol = 1000.0 >> emstep = 0.01 >> >> i found the website and some one said change the table extension to 2 or >> 3 or maybe more, it works for this step, but after performing the >> postion constrains, it got the wrong results. so i guess i will not >> change the table extension, and i do not why it only work for small >> protein not for larger one, and i repeated sevel times, such as changing >> timesteps and rlist and rcoulomb and rvdw to 0.9. still not working. >> could anyone help me to explain this. > > Your system is blowing up due to some non-physical interaction. Tweaking the > table-extension is probably not going to help. Some general references: > > http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off > > http://oldwiki.gromacs.org/index.php/blowing_up > > Without knowing more about how you prepared the system (exact commands), then > you will not likely get much more useful advice. Take a look at where things > are falling apart (atom numbers printed in the .log file) and see if you can > deduce the source of the problem. > > -Justin > >> thank you very much >> Reards, >> Yi >> >> ------------------------------------------------------------------------ >> 您可以借助 Windows Live 整理、编辑和 共享您的照片。 >> <http://www.microsoft.com/china/windows/windowslive/products/photo-gallery-ed >> it.aspx> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://lists.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
