[gmx-users] Problem with Inflategro!!!

[Justin Lemkul]

On 7/18/12 7:07 AM, Manikam Sadasivam Saravanan wrote:
> 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

What does this mean?

> is packed inside. but now  the area per lipid is too low for popc its
> like 0.148 nm2
>

After inflation, the area should be huge.  What was your command line for 
InflateGRO?

If the protein is not in the desired location, you need to use editconf -center 
to adjust its coordinates.  Make sure it is also within a box that matches that 
of the lipid bilayer.

-Justin

> 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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>
>
>

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

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

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