[gmx-users] sphere around a protein
shivangi nangia
shivangi.nangia at gmail.com
Mon May 9 07:01:05 CEST 2011
Hi Justin,
I used 15 nm cubic box and 6 nm shell.
I again tried to insert only 1 histidine molecule in the sphere. I get the
same error
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.
On Sun, May 8, 2011 at 9:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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>
>>
>> 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 <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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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