[gmx-users] Problem with Inflategro!!!

[Manikam Sadasivam Saravanan]

Thanks for the message, I have a .pdb containing my membrane protein
inside the leaflet of popc bilayer, so i wanted to remove the
interacting lipid molecules, hence i used inflategro.

I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce
a protein bilayer system using that, because I wanted to fix/orient my
protein exactly according to my need, so I was using SYBYL to do it.

the box vector values were   11.13710  11.41790   7.60370
and after changing HOH to SOL, my water molecules disappeared as expected.




On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> 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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-- 
MSS