[gmx-users] Problem with Inflategro!!!

[Manikam Sadasivam Saravanan]

no, water problem is solved, but my protein is still out of the bilayer,
When i change:minimize my box vector values and inflate...the protein
is packed inside. but now  the area per lipid is too low for popc its
like 0.148 nm2

On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote:
>>
>> 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.
>>
>>
>
> So is the problem solved then?
>
> -Justin
>
>
>>
>>
>> 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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>>
>>
>>
>>
>
> --
> ========================================
>
> 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