Re: [gmx-users] Deformation of DNA duplex
I am not sure if GROMACS can do that type of analysis. But I think 3DNA should be able to compute the different base pair step parameters. Debayan On Wed, Jul 15, 2015 at 4:12 PM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi all, I have a couple of quick questions. I am simulating DNA duplex with some fullerene derivatives. The fullerenes are expected to accommodate themselves in the major groove of the DNA and I am getting similar results. However, the parallel DNA chains are getting deformed which is also expected. My question is apart from H-bonds is there any way by which one can show that the DNA is getting significantly deformed as compared to its native structure? In the given link below, people have used roll, twist, curl and slides to probe the DNA deformation. Is there any way I can calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB India -- 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] Deformation of DNA duplex
Hi all, I have a couple of quick questions. I am simulating DNA duplex with some fullerene derivatives. The fullerenes are expected to accommodate themselves in the major groove of the DNA and I am getting similar results. However, the parallel DNA chains are getting deformed which is also expected. My question is apart from H-bonds is there any way by which one can show that the DNA is getting significantly deformed as compared to its native structure? In the given link below, people have used roll, twist, curl and slides to probe the DNA deformation. Is there any way I can calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB India -- 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] deformation of DNA duplex
Hi all, I have a couple of quick questions. I am simulating DNA duplex with some fullerene derivatives. The fullerenes are expected to accommodate themselves in the major groove of the DNA and I am getting similar results. However, the parallel DNA chains are getting deformed which is also expected. My question is apart from H-bonds is there any way by which one can show that the DNA is getting significantly deformed as compared to its native structure? In the given link below, people have used roll, twist, curl and slides to probe the DNA deformation. Is there any way I can calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB India -- 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.
