[gmx-users] Position restraints on a pentamer

[plmallip at mail.uh.edu]

Please ignore my previous mail. There was typo error.

Dear colleagues,



                   I want to do MD simulation of only the extracellular
domain of a pentamer, excluding the transmembrane domain. So, I want to
restrain the part of the extracellular domain in contact with the
transmembrane domain. I am using "position restraints" for few of those
residues as well as to the two ends of one of the subunits, in which
there are missing residues.



[ position_restraints ]

; atom  type      fx      fy      fz

   457     1  1000  1000  1000

   459     1  1000  1000  1000

   460     1  1000  1000  1000

   461     1  1000  1000  1000





     After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. 



1) Is this because of imposing position restraints or is it because of the gap in between (due to missing residues) in one of the subunits? 



2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? 



    Coming to the missing residues part, I decided to use distance
restraints between the two ends. Please note that only one of the chain
is in covalently linked with the transmembrane domain. Rest of them
have vanderwaals interactions.



Thanks for any kind of suggestion in this regard.



Prema.

----- Original Message -----
From: <plmallip at mail.uh.edu>
Date: Friday, August 15, 2008 2:00 pm
Subject: Position restraints on a pentamer
To: gmx-users at gromacs.org

> Dear colleagues,
> 
>                    I want to do MD simulation of only the 
> extracellular domain of a pentamer, excluding the transmembrane 
> domain. So, I want to restrain the part of the extracellular 
> domain in contact with the transmembrane domain. I am using 
> "position restraints" for few of those residues as well as to 
> the two ends of one of the subunits, in which there are missing 
> residues.
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>    457     1  1000  1000  1000
>    459     1  1000  1000  1000
>    460     1  1000  1000  1000
>    461     1  1000  1000  1000
> 
> 
>      After few ns of MD, I observed that 3 of the subunits are 
> distorted while the other 2 aren't. 
> 
> 1) Is this because of imposing position restraints or is it 
> because of the gap between two subunits in on the subunits? 
> 
> 2)Is there any other way to restrain (apart from position 
> restraints) the protein for this purpose? 
> 
>     Coming to the missing residues part, I decided to use 
> distance restraints between the two ends. Please note that only 
> one of the chain is in covalently linked with the transmembrane 
> domain. Rest of them have vanderwaals interactions.
> 
> Thanks for any kind of suggestion in this regard.
> 
> Prema.
> 
>
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