On 3/14/20 1:59 AM, Billy Williams-Noonan wrote:
Hi Experts, This is a long-ish e-mail so thank you very much for your time I am using the GROMACS compatible charmm36 forcefield for betapeptides described here: https://gitlab.com/awacha/charmm-beta.ff In merged.rtp I have redefined the MYR residue hoping I could link it to the N-terminus of my b-peptide [ MYR ] [ atoms ] O1 OCL -0.546 1 C1 CL 0.542 2 C2 CA -0.280 3 H2R HAL2 0.090 4 H2S HAL2 0.090 5 C3 CTL2 -0.180 6 H3R HAL2 0.090 7 H3S HAL2 0.090 8 C4 CTL2 -0.180 9 H4R HAL2 0.090 10 H4S HAL2 0.090 11 C5 CTL2 -0.180 12 H5R HAL2 0.090 13 H5S HAL2 0.090 14 C6 CTL2 -0.180 15 H6R HAL2 0.090 16 H6S HAL2 0.090 17 C7 CTL2 -0.180 18 H7R HAL2 0.090 19 H7S HAL2 0.090 20 C8 CTL2 -0.180 21 H8R HAL2 0.090 22 H8S HAL2 0.090 23 C9 CTL2 -0.180 24 H9R HAL2 0.090 25 H9S HAL2 0.090 26 C10 CTL2 -0.180 27 H10R HAL2 0.090 28 H10S HAL2 0.090 29 C11 CTL2 -0.180 30 H11R HAL2 0.090 31 H11S HAL2 0.090 32 C12 CTL2 -0.180 33 H12R HAL2 0.090 34 H12S HAL2 0.090 35 C13 CTL2 -0.180 36 H13R HAL2 0.090 37 H13S HAL2 0.090 38 C14 CTL3 -0.270 39 H14R HAL3 0.090 40 H14S HAL3 0.090 41 H14T HAL3 0.090 42 [ bonds ] O1 C1 C1 C2 C1 +N C2 H2R C2 H2S C2 C3 C3 H3R C3 H3S C3 C4 C4 H4R C4 H4S C4 C5 C5 H5R C5 H5S C5 C6 C6 H6R C6 H6S C6 C7 C7 H7R C7 H7S C7 C8 C8 H8R C8 H8S C8 C9 C9 H9R C9 H9S C9 C10 C10 H10R C10 H10S C10 C11 C11 H11R C11 H11S C11 C12 C12 H12R C12 H12S C12 C13 C13 H13R C13 H13S C13 C14 C14 H14R C14 H14S C14 H14T [ impropers ] C1 C2 +N O1 In ffnonbonded.itp I have added the following dihedral types: C2 C1 +N C 9 0.000000 7.531200 1 C2 C1 +N HN 9 0.000000 7.531200 1 Running pdb2gmx I get the following error: *gmx pdb2gmx -f outpdb.pdb -o pep.pdb -p pep.top -ter* Processing chain 1 'A' (105 atoms, 4 residues) Identified residue MYR1 as a starting terminus. Identified residue B3K4 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for MYR-1 0: Beta3NH3+ 1: Beta2NH3+ 2: Beta23NH3+ 3: B3_NH2 4: B2_NH2 5: B23_NH2 6: 5TER 7: None 7 Start terminus MYR-1: None Select end terminus type for B3K-4 0: BetaCOO- 1: BetaCOOH 2: BetaCT2 3: 3TER 4: None 0 End terminus B3K-4: BetaCOO- Opening force field file ./charmm36_betapep.ff/betaaminoacids.arn Opening force field file ./charmm36_betapep.ff/cyclicbeta.arn Opening force field file ./charmm36_betapep.ff/merged.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 4 residues with 106 atoms Making bonds... Number of bonds was 105, now 105 Generating angles, dihedrals and pairs... Before cleaning: 288 pairs ------------------------------------------------------- Program: gmx pdb2gmx, version 2018.2 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 148) Fatal error: Residue 2 named MYR of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- It seems to be having a problem recognising the link between C1 of Myr and the N-terminus of the next residue (B3K) - is there a file where I can explicitly mention this? Any help would be appreciated - how do I fix this?
The issue comes from whatever the amino acid is; the [impropers] and [cmap] entries specify that -C is needed to impose these bonded interactions. Your MYR residue does not have an atom named C, so you get an error.
The cleanest solution is probably to create a complete residue for a custom residue already linked to MYR (merge MYR with the amino acid). You likely don't want a CMAP on that residue, anyway.
-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.
