To see if complex is stable and to see how it fluctuate in the binding site.
On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/19 10:53 AM, Quin K wrote: > > Hi, > > > > *What should I pick for RMSD analysis of protein ligand complex? * > > *What other analysis can be done for protein ligand complex? * > > Following are the options I have for least square fit and for RMSD > > calculation. > > MPPA is the ligand I used. > > Group 0 ( System) has 50085 elements > > Group 1 ( Protein) has 4590 elements > > Group 2 ( Protein-H) has 2307 elements > > Group 3 ( C-alpha) has 282 elements > > Group 4 ( Backbone) has 846 elements > > Group 5 ( MainChain) has 1127 elements > > Group 6 ( MainChain+Cb) has 1396 elements > > Group 7 ( MainChain+H) has 1399 elements > > Group 8 ( SideChain) has 3191 elements > > Group 9 ( SideChain-H) has 1180 elements > > Group 10 ( Prot-Masses) has 4590 elements > > Group 11 ( non-Protein) has 45495 elements > > Group 12 ( Other) has 31 elements > > Group 13 ( MPPA) has 31 elements > > Group 14 ( NA) has 2 elements > > Group 15 ( Water) has 45462 elements > > Group 16 ( SOL) has 45462 elements > > Group 17 ( non-Water) has 4623 elements > > Group 18 ( Ion) has 2 elements > > Group 19 ( MPPA) has 31 elements > > Group 20 ( NA) has 2 elements > > Group 21 ( Water_and_ions) has 45464 elements > > Group 22 ( Protein_MPPA) has 4621 elements > > > > Thanks & regards! > > What is your objective in calculating RMSD? > > -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.