# [gmx-users] Pulling a ligand out of protein cavity

Shay Teaching shay.teaching at gmail.com
Tue May 31 18:07:33 CEST 2011

```Thanks for you prompt reply - I'll try that and post back.
-SA

On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Shay Teaching wrote:
>
>> Dear gromacs users,
>>
>> I am trying to pull a ligand out of a cavity of a membrane protein (along
>> the Z axis).
>> Problem is, that with every pull settings I have tried the ligand gets
>> "stuck" on the protein's center of mass. How can I make it go all the was to
>> the bulk water?
>> It always gets stuck on the COM. And I've tried using both umbrella and
>> constant force, so I'm getting the feeling that I'm missing something
>> trivial.
>>
>> Here's an example of one set of pull-parameters I tried:
>> ------------------------------->
>> pull             = constant_force
>> pull_geometry    = distance
>>
>
> You can only use the distance method if the distance between pull_group0
> and pull_group1 is constantly decreasing or increasing.  If you're moving
> through a channel, you should use the position method in conjunction with an
> appropriate pull_vec1.
>
>
>  pull_dim         = N N Y
>> pull_start       = yes        ; define initial COM distance > 0
>>
>> pull_ngroups   = 1
>> pull_group0    = Protein
>>
>
> You probably need a better reference group, i.e. some subset of residues
> that forms the entrance or exit from the channel, but you may be able to get
> away with this reference group if you using a more appropriate
> pull_geometry, as suggested above.
>
> -Justin
>
>
>  pull_group1    = Ligand
>> ;pull_rate1    = -0.001        ; 0.01 nm per ps = 10 nm per ns
>> pull_k1        = 1000           ; kJ mol^-1 nm^-2
>> <------------------------------
>>
>> Can anyone help enlighten me as to what I am doing wrong?
>> Thanks,
>> -Shay
>>
>> P.S.
>> Using gromacs 4.0.7.
>>
>>
> --
> ========================================
>
> 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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