Thank you very much, yes normally, the header of pdb file has remark 465 and 470. I just used the modeller loop to add the missing residues according to remark 470, and did not add following remark 465, is it right? because there are only RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER, it does not have atoms. By the way, there is a limit for modeller loop, if I want to addd more resiudes, are there any others softwares which are recommended. Thank you very much Yi
On 03/08/2009 17:12, "Justin A. Lemkul" <jalem...@vt.edu> wrote: > > > Yi Hou wrote: >> 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 >> > > If I'm not mistaken, 1z92 has substantial stretches of missing residues, and > you > probably had to model them in. I'd look at those regions as being potentially > problematic. > >> 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 > > I'd stop and diagnose why the minimization failed. If you can't finish EM, > there is no point in running any sort of dynamics, equilibration or otherwise. > > -Justin > >> Thank you very much >> Yi >> >> >> On 03/08/2009 15:56, "Justin A. Lemkul" <jalem...@vt.edu> 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-o >>> ff >>> >>> 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 gmx-users@gromacs.org >>>> 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 gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> _______________________________________________ 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/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/mailing_lists/users.php