Re: [gmx-users] oplsaa galactose
Hi, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. The set of torsional angle parameters in the paper are given in Kcal/mol, but because I am using OPLS-AA I would need to convert the functions into RB-types, right? Is there a way to convert these functions to RB-types? Or do I convert them from Kcal/mol to KJ/mol? Thanks. Nisha P Quoting nishap.pa...@utoronto.ca: Thanks Justin! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parameters for hexopyronase. I am not sure what the comment below means. Below are extra dihedrals for some special organic molecules. ; Since the atom types are identical to other dihedrals you have to specify ; them explicitly with a define if you happen to simulate this type of molecule. How would I mention it in my rtp file? I don't understand ' specify them explicitly with a define' This is my .rtp for Galactose See examples in aminoacids.rtp, e.g. ARG. -Justin [ GLA ] [ atoms ] Oopls_180 -0.400 1 C1 opls_1950.365 2 H1opls_1960.100 2 O1opls_154 -0.683 2 HO1 opls_1550.418 2 C2 opls_1580.205 3 H2opls_1760.060 3 O2opls_154 -0.683 3 HO2 opls_1550.418 3 C3 opls_1580.205 4 H3opls_1760.060 4 O3opls_154 -0.683 4 HO3 opls_1550.418 4 C4 opls_1580.205 5 H4opls_1760.060 5 O4opls_154 -0.683 5 HO4 opls_1550.418 5 C5 opls_1830.170 6 H5opls_1850.030 6 C6opls_1570.145 7 H61 opls_1760.060 7 H62 opls_1760.060 7 O6opls_154 -0.683 7 HO6 opls_1550.418 7 [ bonds ] OC1 C1 H1 C1 O1 O1 HO1 C1 C2 C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 O4 HO4 C4 C5 C5 C6 C5 O C6 H61 C6 H62 C6 O6 O6 HO6 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] oplsaa galactose
Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parameters for hexopyronase. I am not sure what the comment below means. Below are extra dihedrals for some special organic molecules. ; Since the atom types are identical to other dihedrals you have to specify ; them explicitly with a define if you happen to simulate this type of molecule. How would I mention it in my rtp file? I don't understand ' specify them explicitly with a define' This is my .rtp for Galactose [ GLA ] [ atoms ] Oopls_180 -0.400 1 C1opls_1950.365 2 H1opls_1960.100 2 O1opls_154 -0.683 2 HO1 opls_1550.418 2 C2opls_1580.205 3 H2opls_1760.060 3 O2opls_154 -0.683 3 HO2 opls_1550.418 3 C3opls_1580.205 4 H3opls_1760.060 4 O3opls_154 -0.683 4 HO3 opls_1550.418 4 C4opls_1580.205 5 H4opls_1760.060 5 O4opls_154 -0.683 5 HO4 opls_1550.418 5 C5opls_1830.170 6 H5opls_1850.030 6 C6opls_1570.145 7 H61 opls_1760.060 7 H62 opls_1760.060 7 O6opls_154 -0.683 7 HO6 opls_1550.418 7 [ bonds ] OC1 C1 H1 C1 O1 O1 HO1 C1 C2 C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 O4 HO4 C4 C5 C5 C6 C5 O C6 H61 C6 H62 C6 O6 O6 HO6 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] oplsaa galactose
Thanks Justin! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parameters for hexopyronase. I am not sure what the comment below means. Below are extra dihedrals for some special organic molecules. ; Since the atom types are identical to other dihedrals you have to specify ; them explicitly with a define if you happen to simulate this type of molecule. How would I mention it in my rtp file? I don't understand ' specify them explicitly with a define' This is my .rtp for Galactose See examples in aminoacids.rtp, e.g. ARG. -Justin [ GLA ] [ atoms ] Oopls_180 -0.400 1 C1 opls_1950.365 2 H1opls_1960.100 2 O1opls_154 -0.683 2 HO1 opls_1550.418 2 C2 opls_1580.205 3 H2opls_1760.060 3 O2opls_154 -0.683 3 HO2 opls_1550.418 3 C3 opls_1580.205 4 H3opls_1760.060 4 O3opls_154 -0.683 4 HO3 opls_1550.418 4 C4 opls_1580.205 5 H4opls_1760.060 5 O4opls_154 -0.683 5 HO4 opls_1550.418 5 C5 opls_1830.170 6 H5opls_1850.030 6 C6opls_1570.145 7 H61 opls_1760.060 7 H62 opls_1760.060 7 O6opls_154 -0.683 7 HO6 opls_1550.418 7 [ bonds ] OC1 C1 H1 C1 O1 O1 HO1 C1 C2 C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 O4 HO4 C4 C5 C5 C6 C5 O C6 H61 C6 H62 C6 O6 O6 HO6 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
