[gmx-users] How to parametrize a new molecule?
Dear users, I want to perform a simulation of a molecule inside DNA. I'm probably going to use CHARMM for DNA. But how do I parametrize the molecule? Thanks in advance. Yours, Herbert Georg -- 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] How to parametrize a new molecule?
On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: Dear users, I want to perform a simulation of a molecule inside DNA. I'm probably going to use CHARMM for DNA. But how do I parametrize the molecule? http://cgenff.umaryland.edu/ -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] How to parametrize a new molecule?
Thanks, Justin! Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul escreveu: > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > Dear users, > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > going > > to use CHARMM for DNA. But how do I parametrize the molecule? > > http://cgenff.umaryland.edu/ > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] How to parametrize a new molecule?
Hello Herbert, Not related to your question, but be careful if you are going to use CHARMM36 force field for DNA, as a recent study ( https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does not preserve DNA stability at a longer time scale, in case you are going to do so. Best, Mahdi On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg wrote: > Thanks, Justin! > > > > Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul > escreveu: > > > > > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > > Dear users, > > > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > > going > > > to use CHARMM for DNA. But how do I parametrize the molecule? > > > > http://cgenff.umaryland.edu/ > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > == > > > > -- > > 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. -- 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] How to parametrize a new molecule?
Thanks, Mahdi. I'm aware of that study. Actually it's because of it that I have chosen the latest CHARMM27 for the simulations. Best, Herbert Em sáb., 4 de abr. de 2020 às 12:57, Mahdi Bagherpoor escreveu: > Hello Herbert, > > Not related to your question, but be careful if you are going to use > CHARMM36 force field for DNA, as a recent study ( > https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does > not preserve DNA stability at a longer time scale, in case you are going to > do so. > > Best, > Mahdi > > On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg > wrote: > > > Thanks, Justin! > > > > > > > > Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul > > escreveu: > > > > > > > > > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > > > Dear users, > > > > > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > > > going > > > > to use CHARMM for DNA. But how do I parametrize the molecule? > > > > > > http://cgenff.umaryland.edu/ > > > > > > -Justin > > > > > > -- > > > == > > > > > > Justin A. Lemkul, Ph.D. > > > Assistant Professor > > > Office: 301 Fralin Hall > > > Lab: 303 Engel Hall > > > > > > Virginia Tech Department of Biochemistry > > > 340 West Campus Dr. > > > Blacksburg, VA 24061 > > > > > > jalem...@vt.edu | (540) 231-3129 > > > http://www.thelemkullab.com > > > > > > == > > > > > > -- > > > 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. > -- > 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.