Re: [gmx-users] CMAP entries for D-residues with GROMACS (Justin Lemkul)
OK I see thank you, Justin Bye On 3/2/18 10:50 AM, ABEL Stephane wrote: > Dear all, > > I am interested to simulate a system with gramicidin A that contains D-AAs > (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp > file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this > because I see that the CHARMM force field library contains a file > (toppar_all36_prot_mod_d_aminoacids.str) where the CMAP parameter seem to be > redefined. The parameters are not "redefined," they are given for the D-amino acids, which have a different C-alpha type (CTD1 instead of CT1). The latest CHARMM36 port supports D-amino acids, with the exception of the .hdb file, which does not have entries for them. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] CMAP entries for D-residues with GROMACS
On 3/2/18 10:50 AM, ABEL Stephane wrote: Dear all, I am interested to simulate a system with gramicidin A that contains D-AAs (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this because I see that the CHARMM force field library contains a file (toppar_all36_prot_mod_d_aminoacids.str) where the CMAP parameter seem to be redefined. The parameters are not "redefined," they are given for the D-amino acids, which have a different C-alpha type (CTD1 instead of CT1). The latest CHARMM36 port supports D-amino acids, with the exception of the .hdb file, which does not have entries for them. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] CMAP entries for D-residues with GROMACS
Dear all, I am interested to simulate a system with gramicidin A that contains D-AAs (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this because I see that the CHARMM force field library contains a file (toppar_all36_prot_mod_d_aminoacids.str) where the CMAP parameter seem to be redefined. Thank you for you response. Stéphane -- 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.
