On 8/14/17 8:15 AM, ZHANG Cheng wrote:
Dear Gromacs, My MD contains a protein (442 residues) and 203 free glycines. The numbering of the residues is: 1-442: the protein residues 443-645: the 203 free glycines When I use the "rms" command, all the 645 residues are considered as the "Protein" category. I cannot find an option that could only calculate rmsd for the first 442 residues in my proteins. How can I do this? Thank you.
Create an index group with gmx make_ndx or gmx select. -Justin
Group 0 ( System) Group 1 ( Protein) Group 2 ( Protein-H) Group 3 ( C-alpha) Group 4 ( Backbone) Group 5 ( MainChain) Group 6 ( MainChain+Cb) Group 7 ( MainChain+H) Group 8 ( SideChain) Group 9 ( SideChain-H) Group 10 ( Prot-Masses) Group 11 ( non-Protein) Group 12 ( Water) Group 13 ( SOL) Group 14 ( non-Water) Group 15 ( Ion) Group 16 ( NA) Group 17 ( CL) Group 18 ( Water_and_ions)
-- ================================================== 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.
