Re: [gmx-users] CG (MARTINI) parameters for RNA
Hi Tom, Thanks for your replay. From the paper (DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. ) I understand that the DNA CG particles where identical to the one used for lipids and protein, am I correct? Also, they had used elastic network to hold them in place (instead of Secondary Structure used in proteins). Best, Itamar On 28/05/10 12:11 AM, Thomas Piggot wrote: Hi, The DNA parameters for use with the MARTINI forcefield are not publicly available to download at the moment, however they will be available very soon. I (or someone else from the Khalid group) will let the list know when and where they have been made available. Cheers Tom Itamar Kass wrote: Shalom all, I wish to try and simulate a protein with few RNA bases attached. As I favour speed over accuracy in this case I wish to use the MARTINI model. I could not find RNA/DNA parameters, but noticed that on the site there is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP. DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. I wonder if someone had those parameters already implemented into the model? It will be nice to get it nicely packed. Or maybe even better, are there any beta parameters to RNA/DNA in a new MARTINI force field? All the best, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu.au -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG (MARTINI) parameters for RNA
Hi, The DNA parameters for use with the MARTINI forcefield are not publicly available to download at the moment, however they will be available very soon. I (or someone else from the Khalid group) will let the list know when and where they have been made available. Cheers Tom Itamar Kass wrote: Shalom all, I wish to try and simulate a protein with few RNA bases attached. As I favour speed over accuracy in this case I wish to use the MARTINI model. I could not find RNA/DNA parameters, but noticed that on the site there is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP. DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. I wonder if someone had those parameters already implemented into the model? It will be nice to get it nicely packed. Or maybe even better, are there any beta parameters to RNA/DNA in a new MARTINI force field? All the best, Itamar -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CG (MARTINI) parameters for RNA
Shalom all, I wish to try and simulate a protein with few RNA bases attached. As I favour speed over accuracy in this case I wish to use the MARTINI model. I could not find RNA/DNA parameters, but noticed that on the site there is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP. DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. I wonder if someone had those parameters already implemented into the model? It will be nice to get it nicely packed. Or maybe even better, are there any beta parameters to RNA/DNA in a new MARTINI force field? All the best, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu.au -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
