[gmx-users] bad bond in polymer

[Justin A. Lemkul]

nicegromacs wrote:
> Hi,
>  
> the bad bond appear in the topology (.top) file.
>  

Then it is something you have added.  If you want any useful advice, post the 
.rtp entries you are using.

-Justin

> veduardo.
> 
>  Lab. de  Fisicoquímica Molecular
>  
> Facultas de Ciencias
>  
> Universidad de Chile
> 
> *From:* nicegromacs <mailto:nicegromacs at live.cl>
> *Sent:* Wednesday, August 12, 2009 8:28 PM
> *To:* gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> *Subject:* [gmx-users] bad bond in polymer
> 
> Hi gmx-users,
> 
> I am building a polymer and I've added the monomer unit to the 
> .rtp file. The final structure appears with an undesired bond between 
> the monomer units at the extremes of the polymer.
> How can I prevent the monomers at the end forming the bond?
> 
> I have read other post like 
> http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html  but  
> can not avoid this problem .
> 
> Thank you in advance
> 
> veduardo.
> 
> Lab. de  Fisicoquímica Molecular
> 
> Facultas de Ciencias
> 
> Universidad de Chile
> 
>  
> 
>  
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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