Dear Justin, No.
I am still preparing the system. I want the protein in the solvent sphere. On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shivangi nangia wrote: > >> Hello, >> >> Thanks Justin, I am getting somewhere but still running into problems. >> >> Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 >> water-methanol mixture) in 12 nm box. >> I did the following: >> editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro >> genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro >> >> >> Then, used genbox -cp protein.gro -cs sphere.gro >> with only 1 molecule of histidine I get the same error as with >> polyhistidine ( 20 ) >> >> Fatal error: >> One of the box vectors has become shorter than twice the cut-off length or >> box_yy-|box_zy| or box_zz has become smaller than the cut-off. >> >> > I presume this is from mdrun? Your system is collapsing. Without an .mdp > file, it is not possible to diagnose anything. > > -Justin > > How can I resolve this? >> >> help needed. >> >> Thanks, >> SN >> >> On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> shivangi nangia wrote: >> >> Hi Justin and other gmx-users, >> >> I want to make a sphere around a protein (5nm).with Li ions and >> anions. >> >> Justin, as you had suggested to use genbox -shell option, I >> tried using it but i realized that since my protein is a long >> tube like structure, the shell option generated a cyclinder >> around the protein. >> >> The solvent around the protein is 1:1 water-methanol >> (pre-prepared mixture n a gro file) >> >> If I try to start with a ion and solvate it with my solvent (1:1 >> water methanol) using -shell option, I do get a sphere but then >> I am unable to insert the protein in the system. >> >> >> And why not? >> >> genbox -cp protein.gro -cs sphere.gro >> >> should do exactly what you want, provided the sphere is large enough >> for the protein. >> >> -Justin >> >> >> Is there another feasible route to get to my desired >> configuration of the system ? >> >> Thanks in advance >> >> >> Best, >> SN >> >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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