[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 <
sarathchandradantu at 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 <antara.mazumdar at igib.in> 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
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.