[gmx-users] Problem with Inflategro!!!

[Justin Lemkul]

On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote:
> Hi,
>
> I am a new user to Gromacs, just started exploring it since 3 months, Thanks
> to Justin, In-fact i learned a lot form his tutorial using KALP protein in
> dppc.
>
> Currently I am working with simulation of Membrane protein in a popc
> bilayer, its a complete membrane protien which lies in one of the leaflet of
> the bilayer. I placed my protein inside the popc bilayer (developed using
> Charmm GUI) in the exact position using SYBYL , same as what is done in the
> "building unit cell" part of the KALP tutorial and with the satisfied
> orientation of protein.
> Then the final pdb with protein, popc and water molecules is used to produce
> a .gro file using pdb2gmx tool.
>
> later I tried to do "Inflategro" to remove the unwanted lipid molecules
> interacting with my protein, but i was not successful because, when i
> visualize my .gro file of system-inflated, my water molecules are still
> present and my protein is out of from my lipid box and when i shrink the
> bilayer, the protein is completely lost!
> could you please give me an idea to do a proper inflated and deflate in my
> case?  thank you!!

Why do you even need InflateGRO?  Is there some reason CHARMM-GUI produces an 
unsatisfactory result?  I thought that it could produce membrane protein 
systems, in which case you don't need to do anything.

Unfortunately, at this point, it's impossible to know what's going wrong.  There 
are too many weird things going on, none of which should be happening with a 
sensible input.  A few things to consider:

1. What are the box vectors in the .gro file produced by pdb2gmx?
2. Are the water molecules named properly?  InflateGRO expects them to be named 
SOL in order to work.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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