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. How can I resolve this? help needed. Thanks, SN On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul <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 | (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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