On 11/26/17 6:06 PM, MD wrote:
Hi, I had to repost this cause of the size of the previous thread. I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp, line 52165]: Unknown cmap torsion between atoms 3022 3024 3026 3046 3049" The 3022 3024 3026 3046 3049 in the itp files referred to the backbone (C-N-CA-C-N) of three connected residues R-W-T.. I found out it is the W that causing issue. I am not sure why it has one CC, two OT1 instead of one C and O like the rest of the Trp residues in the protein. This is the only Trp that has these parameters. Any suggestions?
This is the C-terminal Trp residue, hence the carbonyl becomes a carboxylate. There should not be a CMAP generated for a C-terminal residue and pdb2gmx should have removed that interaction.
If this is the residue preceding CSO, then you are getting a false chain termination because you haven't added CSO to residuetypes.dat.
-Justin
residue 196 TRP rtp TRP q -1.0 3024 NH1 196 TRP N 3024 -0.47 14.007 ; qtot 8.53 3025 H 196 TRP HN 3025 0.31 1.008 ; qtot 8.84 3026 CT1 196 TRP CA 3026 0.07 12.011 ; qtot 8.91 3027 HB1 196 TRP HA 3027 0.09 1.008 ; qtot 9 3028 CT2 196 TRP CB 3028 -0.18 12.011 ; qtot 8.82 3029 HA2 196 TRP HB1 3029 0.09 1.008 ; qtot 8.91 3030 HA2 196 TRP HB2 3030 0.09 1.008 ; qtot 9 3031 CY 196 TRP CG 3031 -0.03 12.011 ; qtot 8.97 3032 CA 196 TRP CD1 3032 -0.15 12.011 ; qtot 8.82 3033 HP 196 TRP HD1 3033 0.22 1.008 ; qtot 9.04 3034 NY 196 TRP NE1 3034 -0.51 14.007 ; qtot 8.53 3035 H 196 TRP HE1 3035 0.37 1.008 ; qtot 8.9 3036 CPT 196 TRP CE2 3036 0.24 12.011 ; qtot 9.14 3037 CPT 196 TRP CD2 3037 0.11 12.011 ; qtot 9.25 3038 CAI 196 TRP CE3 3038 -0.25 12.011 ; qtot 9 3039 HP 196 TRP HE3 3039 0.17 1.008 ; qtot 9.17 3040 CA 196 TRP CZ3 3040 -0.2 12.011 ; qtot 8.97 3041 HP 196 TRP HZ3 3041 0.14 1.008 ; qtot 9.11 3042 CAI 196 TRP CZ2 3042 -0.27 12.011 ; qtot 8.84 3043 HP 196 TRP HZ2 3043 0.16 1.008 ; qtot 9 3044 CA 196 TRP CH2 3044 -0.14 12.011 ; qtot 8.86 3045 HP 196 TRP HH2 3045 0.14 1.008 ; qtot 9 3046 CC 196 TRP C 3046 0.34 12.011 ; qtot 9.34 3047 OC 196 TRP OT1 3047 -0.67 15.9994 ; qtot 8.67 3048 OC 196 TRP OT2 3048 -0.67 15.9994 ; qtot 8
-- ================================================== 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.
