[gmx-users] Problem with Inflategro!!!

[Justin Lemkul]

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
>>
>> ========================================
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>
>
>

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

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

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