[gmx-users] bilayer thickness 100ns membrane protein

Tue Sep 18 13:34:15 CEST 2018

Thnxx 4 your reply

On Tue, Sep 18, 2018, 4:37 PM Stephani Macalino <stephanimacalino at gmail.com>
wrote:

> Hello,
> I made sure that my protein is oriented in the z-axis using gmx editconf.
> My protein has extracellular domain. After orientation, you can check the
> structure if the EC domain is outside the membrane. If not, you can edit
> the Z-coordinate to move it along the z-axis.
> The topology file is automatically prepared by the charmm-gui.
> Regards,
> Stephani
>
> On Tue, 18 Sep 2018 at 17:00, Bratin Kumar Das <
> 177cy500.bratin at nitk.edu.in>
> wrote:
>
> > Dear stephani,
> >                          Did u modify anything in your initial protein
> > coordinate? Do u have any extracellular domain in your protein? How you
> > made the topology file after preparing the system in CHARMM-gui
> >
> > On Tue, Sep 18, 2018, 12:25 PM Stephani Macalino <
> > stephanimacalino at gmail.com>
> > wrote:
> >
> > > Hi Bratin,
> > > Sorry, I can't advise you on this. I am a newbie in this field as well.
> > > You might want to check charmm-gui for any contact information, and
> send
> > > them your question.
> > > In my experience, they reply quite fast.
> > >
> > > On Tue, 18 Sep 2018 at 15:34, Bratin Kumar Das <
> > > 177cy500.bratin at nitk.edu.in>
> > > wrote:
> > >
> > > > Dear Stephani,
> > > >                         I tried charmm-gui to pack the lipid bilayer
> > > > arround my protein. But charmm gui is giving fatal error. what
> possible
> > > > reason can be there for this fatal error.
> > > >
> > > > On Tue, Sep 18, 2018 at 11:01 AM, Stephani Macalino <
> > > > stephanimacalino at gmail.com> wrote:
> > > >
> > > > > Hello Bratin,
> > > > > I used charmm-gui to generate the MD input files and used CHARMM36
> as
> > > > > forcefield.
> > > > > Then I used gromacs for the MD production run for 100ns.
> > > > > Once I got the trajectory files, I did the membrane analysis using
> a
> > > tcl
> > > > > script and gridmat.
> > > > > I followed the gromacs tutorial starting from the minimization.
> > > > > Regards,
> > > > > Stephani
> > > > >
> > > > >
> > > > > On Tue, 18 Sep 2018 at 14:25, Bratin Kumar Das <
> > > > > 177cy500.bratin at nitk.edu.in>
> > > > > wrote:
> > > > >
> > > > > > Dear Stephani,
> > > > > >                        Can u please tell me how you did the
> > > simulation
> > > > > and
> > > > > > what forcefield you used for your system. Did you followed the
> same
> > > > > > tutorial explained by justin lemkul
> > > > > >
> > > > > > On Sun, Sep 16, 2018 at 9:46 PM, Stephani Macalino <
> > > > > > stephanimacalino at gmail.com> wrote:
> > > > > >
> > > > > > > Hello,
> > > > > > > I ran a 100ns MD or a membrane protein and am now analyzing the
> > APL
> > > > and
> > > > > > > bilayer thickness from the trajectory file of 50,000 frames.
> > > > > > > When I graphed the values, around 20 to 30k frames in (and some
> > > > frames
> > > > > > > along 40k) the value jumps from 40 to 70. The rest of the
> frames
> > > have
> > > > > > > pretty similar value at 40.
> > > > > > > Can you provide any idea why this happens?
> > > > > > > I already used trjconv in for my system before doing this.
> > > > > > > Should I run it for a longer time?
> > > > > > > Hope you can help. Thank you!
> > > > > > > Regards,
> > > > > > > Stephani
> > > > > > > --
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