shivangi nangia wrote:
Dear Justin,
No.
I am still preparing the system. I want the protein in the solvent sphere.
I see now. You're setting a 12-nm cubic box, but then using a shell of 6 nm,
which causes neighbor searching to occur throughout the entire box. The maximum
value of -shell must be less than 1/2 the shortest box vector, so either set up
a larger box, or a smaller value of -shell.
-Justin
On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto: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>
<mailto: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> <http://vt.edu> | (540)
231-9080 <tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
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========================================
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
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========================================
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
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