[gmx-users] Restrain free energy

[hoangtung9597]

In the topology .top i see that intramolecular interaction. With bond 2 angle ,3 dihedral. And turn on lamda-bond. I don't know how can i get this infomation for my protein ligand. So instead, i using gmx genstr 1000 1000 1000 and include it to topol.top to running. The result very dissapointed, and i don have this dental gibb restrain... !  Normally, what would you do ?
-------- Tin nhắn gốc --------Từ: asaffarhi at post.tau.ac.il Ngày: 16/09/2018  11:59  (GMT+07:00) Đến: gromacs.org_gmx-users at maillist.sys.kth.se Chủ đề: Re: [gmx-users] Restrain free energy 
I assume that the motivation is that the ligand will be in the right  
place for binding when transforming from vacuum to protein. Maybe in  
this case it is ok and it's not always the case. Regarding the  
technical details you can try to follow the steps or wait for another  
response.

Best,
Asaf
Quoting hoangtung9597 <hoangtung9597 at gmail.com>:

> Thank you, I restrain by gmx genrestr. Position restrain.  Can i ask  
> you if i remove restrain protein ligand, what would happen and does  
> it still true result ?I don't know how to get bond, angle, dihedral  
> to restrain @. at . I just have run without restrain and result is same  
> with tutorial ? I don't know why.
> -------- Tin nhắn gốc --------Từ: asaffarhi at post.tau.ac.il Ngày:  
> 16/09/2018  10:32  (GMT+07:00) Đến: gmx-users at gromacs.org Chủ đề:  
> Re: [gmx-users] Restrain free energy
> Hi,
>
> You can put the numbers in
> https://www.wolframcloud.com/objects/asaf.farhi/test/originalDeployment
> and get Helmholtz free energy of restraints. Alternatively, you can 
> remove the bond angle and dihedral angle term to get their 
> Helmholtz/Gibbs free energies.
> Based on NJP A. Farhi and B. Singh 2016
>
> Best,
> Asaf
> Quoting hoangtung9597 <hoangtung9597 at gmail.com>:
>
>> I'm conflic now. Help me!!That i run free energy protein ligand T4 
>> tutorial, but i can't caculate dental Gibb restrain ? Can you 
>> help.me. thank you so much.
>>
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