Fw: [gmx-users] position restraints

[Justin Lemkul]

On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> The inclusion part was edited again in original top file. I dont know why
> I had written that! Sorry.
> But about last itp files, which you mentioned that they are created
> incorrectly, 1) I 'd like to know what itp file should be created? In my
> own, I just included the chain_B.itp file with the same numbering as the
> chain_A.itp file.
>

I don't really know what that means. You should be using the files pdb2gmx
gave you, at least until you understand how all of this works. You should
not have to deal with anything related to restraining the protein. Hence
why I've suggested that you start over.


> 2) One more thing, restraints for both chains are brought just one time in
> the processed.top file? I thought after each chain, the restraints which
> are included should be brought and written in processed.top file!!!
>
>
They should. But what you showed makes no sense. Restraints can't
correspond to atoms that don't exist and there should only ever be on [
position_restraints ] directive per [ moleculetype ].

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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