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 <jalem...@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 <jalem...@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
========================================
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