[gmx-users] I: How to rolled up a polymer chain

[Sathish Kumar]

Add the parameters for LIG residue in force filed. In that give information
about the LIG in
rtp file
nonbonded file
bonded file
I think then it will work.

On Mon, Sep 22, 2014 at 5:46 AM, marcello cammarata <mstaxmarcello at yahoo.it>
wrote:

>
> Hi,
>  i had checked all the archives, i have read about 100posts in the last 2
> month.
> Nobody have problem similar to mine.
> Problem for me are Two.
> 1- instead i am a doctor, i am not able to find the right advice at your
> site.
> 2- In your site there is no space for begginer user.
>
> The main pages where i checked are:
> Residue
> Chain
> Polyethylene (PE) simulations in Gromacs - please!
> .rtp File
> Force Fields
> Adding a Residue to a Force Field
> Modifying a force field
>
> But i don't have find any suggestion for my problem.
> Is there an other blog, that i can't see.
> i have several of problem with Gromacs,
> - in Cygwin it doen't work, i got a "bash" comand
> - the topology need a lig parameters.
>
> one more time, below there is my post. I wpould like if you can help me to
> solve this question, instead i can try to use an othere MD software.
>
>
> MARCELLO CAMMARATA
> Ing., Ph.D.,
>
>  3208790796
>
>
> Il Lunedì 22 Settembre 2014 14:20, marcello cammarata <
> mstaxmarcello at yahoo.it> ha scritto:
>
>
>
>
>
> My goal, for now, is to model a polimer (nylon-6) chain, and to find the
> equilibrium position of the chain considering the capacity to be rolled up
> itself.
> I had create a pdb file using Avogadro software, but when i go to gromacs
> to input the
>  data using the function pdb2gmx And indipendently of the force field that
> i
>                           choose i get :that "Residue LIG not found".
>
> How to solve this?
> thanks
>
>
>
> MARCELLO CAMMARATA
> Ing., Ph.D.,
>
> 3208790796
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-- 
regards
M.SathishKumar