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