Hi, Please correct me if I am wrong.
In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all the ions that I had added in the box? Some might still be in open space of the box? Thanks, SN On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Justin A. Lemkul wrote: > >> >> >> shivangi nangia wrote: >> >>> Hi Justin, >>> >>> Thanks a lot! >>> Things worked. >>> >>> Now I, however, have a different problem in extension to what I am doing. >>> >>> I was able to created a sphere of water and methanol around a polypeptide >>> and 1 Li+ ion. >>> >>> editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro >>> genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro >>> genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro >>> editconf -f his20.gro -d 0 -o onlyhis.gro >>> editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro >>> genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro >>> >>> >>> Now I need to add few more Li ions and anions in the sphere. >>> >>> I tried doing that, >>> genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top >>> >>> (1dhb.gro is 2,5-dihydrobenzoic acid anion) >>> >>> But, since the sphere 6sys.gro is essentially in a box, the dhb anions >>> ...some got randomly placed inside the sphere and some in the open spaces of >>> the box in which 6sys.gro is sitting. >>> >>> How can I place all the anions and then Li+ ions specifically inside the >>> sphere? >>> >>> >> That's what genion is for. >> > > I take that back, genion doesn't work for polyatomic ions. The better > approach is to construct your system with solute, ions (which in this case > are just other molecules floating around), etc, before adding the sphere of > solvent. > > > -Justin > > -- > ======================================== > > 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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