Re: [gmx-users] sphere around a protein

Justin A. Lemkul Sun, 08 May 2011 18:33:24 -0700


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 1:1water-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 withpolyhistidine ( 20 )
Fatal error:
One of the box vectors has become shorter than twice the cut-off lengthor 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>> 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> | (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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