[gmx-users] sphere around a protein

Justin A. Lemkul jalemkul at vt.edu
Wed May 25 21:43:42 CEST 2011

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 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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