[gmx-users] Position restraints on a pentamer

[Justin A. Lemkul]

plmallip at mail.uh.edu wrote:
> 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.

Can you explain what you mean by distorted?  Or post images online somewhere?

> 
> 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?

Potentially one or the other, or even both.  In science, we have to eliminate 
variables, so you may want to try one of two things (if not both, ultimately):

1. Remove position restraints.
2. Fix the missing residues in the model.

Depending on what you're interested in, either might be a viable option.  I 
would think you'd like to rebuild the missing residues, unless you think they 
will have absolutely no effect on the dynamics.

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

There is an option within the .mdp file called freezegrps.  Note that this 
option doesn't work well when applying pressure coupling.

-Justin

> 
>     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.
>  >
>  >
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================