Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Antara mazumdar]

Dear users,

Is there any script available to calculate % occupancy of residues with
respect to time? This in continuation with my previous query on percentage
of protein in contact with membrane??

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Thu, May 19, 2016 at 6:35 PM, Antara mazumdar 
wrote:

> Dear gromacs users,
>
> I have a peripheral membrane protein which I have simulated using Charmm
> 36 in a mixed lipids bilayer. I want to calculate the percentage of protein
> in contact with membrane wrt time. I already have residue wise distances
> from membrane calculated.
>
> Can anyone suggest me how to go about it after this?
>
> Antara Mazumdar
>
> ISCB SC RSG-India
>
> Core Committee Member
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Tsjerk Wassenaar]

Hi Antara,

You can also simply calculate the ratio of buried surface area to total
surface area, which you can both get with gmx sasa

Cheers,

Tsjerk

On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra <
sarathchandrada...@gmail.com> wrote:

> You can use g_contacts tool which will give you list of residues which are
> in contact with the membrane and their frequencies. You might have to write
> an overhead script to convert the residues in contact to %Protein in
> contact
>
> http://www.sciencedirect.com/science/article/pii/S0010465513002464
>
> Regards,
>
> Sarath
>
> --
> Sarath Chandra Dantu, PhD, ELS
> Room No. 606, New BSBE Building
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> Powai Mumbai, 400-076, India
>
>
> On 19 May 2016 at 18:35, Antara mazumdar  wrote:
>
> > Dear gromacs users,
> >
> > I have a peripheral membrane protein which I have simulated using Charmm
> 36
> > in a mixed lipids bilayer. I want to calculate the percentage of protein
> in
> > contact with membrane wrt time. I already have residue wise distances
> from
> > membrane calculated.
> >
> > Can anyone suggest me how to go about it after this?
> >
> > Antara Mazumdar
> >
> > ISCB SC RSG-India
> >
> > Core Committee Member
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Sarath Chandra]

You can use g_contacts tool which will give you list of residues which are
in contact with the membrane and their frequencies. You might have to write
an overhead script to convert the residues in contact to %Protein in contact

http://www.sciencedirect.com/science/article/pii/S0010465513002464

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 19 May 2016 at 18:35, Antara mazumdar  wrote:

> Dear gromacs users,
>
> I have a peripheral membrane protein which I have simulated using Charmm 36
> in a mixed lipids bilayer. I want to calculate the percentage of protein in
> contact with membrane wrt time. I already have residue wise distances from
> membrane calculated.
>
> Can anyone suggest me how to go about it after this?
>
> Antara Mazumdar
>
> ISCB SC RSG-India
>
> Core Committee Member
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Help required for calculation of protein coverage % wrt time

[Antara mazumdar]

Dear gromacs users,

I have a peripheral membrane protein which I have simulated using Charmm 36
in a mixed lipids bilayer. I want to calculate the percentage of protein in
contact with membrane wrt time. I already have residue wise distances from
membrane calculated.

Can anyone suggest me how to go about it after this?

Antara Mazumdar

ISCB SC RSG-India

Core Committee Member
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.