[gmx-users] Problem with Inflategro!!!
Manikam Sadasivam Saravanan
saravanan.ms3 at gmail.com
Wed Jul 18 13:48:13 CEST 2012
my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC
14 system_inflated.gro 5 area.dat
my gro file looks like,
membrane protein in POPC 121-310KWITNOIONS
59522
1SER N 1 -2.092 -1.832 -1.359
1SER HT1 2 -2.149 -1.861 -1.436
1SER HT2 3 -2.150 -1.809 -1.281
1SER CA 4 -2.002 -1.942 -1.322
...............
91ILE OT1 1527 0.033 1.945 -1.049
91ILE OT2 1528 0.057 1.922 -1.267
continued by popc and sol
1POPC N 1 2.963 -2.658 2.064
1POPC C12 2 3.003 -2.713 2.196
1POPC C13 3 2.954 -2.509 2.062
.........
8764SOL OW57992 3.731 3.721 -2.405
8764SOL HW157993 3.749 3.653 -2.341
8764SOL HW257994 3.723 3.802 -2.353
11.13710 11.41790 7.60370
when I inflate with box vectors value 11.13710 11.41790 7.60370, my
protein is out of inflated lipid boundary. if i change my value to
1.39213 1.42723 0.00000 (dividing above value by half and half),
now my protein is at the center of inflated popc. but the area per
lipid even after inflation is still only 0.148 nm2.
should i use editconf with the whole .gro file containing protein,
popc or i have to separate my protein only as a new.gro file and
perform editconf and then cat?
thanks for the suggestions!
On Wed, Jul 18, 2012 at 1:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ========================================
>>>>>
>>>>>
>>>>> --
>>>>> 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
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>>>>> * 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
>>>
>>> ========================================
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> * Please search the archive at
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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
>
> ========================================
>
>
> --
> 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!
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--
MSS
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