[gmx-users] sphere around a protein

Justin A. Lemkul jalemkul at vt.edu
Wed May 25 21:40:37 CEST 2011

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.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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