[gmx-users] Re: distance restraints for atoms on 2 chains

[Justin A. Lemkul]

pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a 
merged [moleculetype] to apply distance restraints.  If you're just trying to 
use a harmonic potential to define some sampling distance (for US), then 
distance restraints are not necessary, just apply the pull code.

-Justin

Sai Pooja wrote:
> Also, the chains do not diffuse apart in time since they are position 
> restrained(some parts of each chain are ...)
> 
> On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <saipooja at gmail.com 
> <mailto:saipooja at gmail.com>> wrote:
> 
>     Hi,
>      
>     I have 5 chains in my Protein. I want to apply distance restraints
>     for doing Umbrella Sampling for 2 atoms on different chains. Is
>     there a way to do this since the two chains have separater itp files.
>      
>     Pooja
> 
>     -- 
>     Quaerendo Invenietis-Seek and you shall discover.
> 
> 
> 
> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
> 

-- 
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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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