Hi Justin, I added the CSO to residuetypes.dat in my local computer and it worked now. I then tried to copy the modified "residuetypes.dat" to the ff folder on the server computer, but the server computer gromacs wouldn't give option to choose which residuetypes.dat to use. Do you know how to let it choose instead of using its original one by default? Thanks, Ming
On Sun, Nov 26, 2017 at 6:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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. -- 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.
