Dear gromacs users, I have done simulations of 20 residue length of peptide for 100ns. I want to find hydrogen bonds for residue GLU-7. The topology information for this residue as follow.
; residue 7 GLU rtp GLU q -1.0 121 opls_238 7 GLU N 39 -0.5 14.0067 ; qtot 4.5 122 opls_241 7 GLU H 39 0.3 1.008 ; qtot 4.8 123 opls_224B 7 GLU CA 39 0.14 12.011 ; qtot 4.94 124 opls_140 7 GLU HA 39 0.06 1.008 ; qtot 5 125 opls_136 7 GLU CB 40 -0.12 12.011 ; qtot 4.88 126 opls_140 7 GLU HB1 40 0.06 1.008 ; qtot 4.94 127 opls_140 7 GLU HB2 40 0.06 1.008 ; qtot 5 128 opls_274 7 GLU CG 41 -0.22 12.011 ; qtot 4.78 129 opls_140 7 GLU HG1 41 0.06 1.008 ; qtot 4.84 130 opls_140 7 GLU HG2 41 0.06 1.008 ; qtot 4.9 131 opls_271 7 GLU CD 42 0.7 12.011 ; qtot 5.6 132 opls_272 7 GLU OE1 42 -0.8 15.9994 ; qtot 4.8 133 opls_272 7 GLU OE2 42 -0.8 15.9994 ; qtot 4 134 opls_235 7 GLU C 43 0.5 12.011 ; qtot 4.5 135 opls_236 7 GLU O 43 -0.5 15.9994 ; qtot 4 Kindly suggest me how to create index file for this residue. Thanks in advance Surya Graduate student India. -- 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.
