On 8/2/19 12:22 AM, Joseph,Newlyn wrote:
Hello, I'm running into the following error when trying to pdb2gmx my PDB file. Program gmx pdb2gmx, VERSION 5.1.4 Source code file: /gpfs/apps/hpc.rhel7/Packages/Apps/Gromacs/5.1.4/Dist_514/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, line: 645 Fatal error: Residue 'C' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors? I presume I'm naming my residues incorrectly, but upon closer inspection of the merged.rtp file within the forcefield, I see no section for RNA residues. I'm attempting to simulate an RNA that has the following as the first couple lines in the PDB:
In CHARMM, both DNA and RNA are named ADE, CYT, GUA, THY/URA and are generated as RNA. One then patches the RNA residue to become DNA by removing the 2'-OH. We can't do this in GROMACS, so there are fixed residue names.
RNA: ADE, CYT, GUA, URA DNA: DA, DC, DG, DT These are all in merged.rtp. -Justin
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON OCT, 26. 2018. JOB REMARK READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE REMARK DATE: 10/27/18 0:52: 0 CREATED BY USER: apache ATOM 1 H5T C A 1 -29.997 -20.428 3.250 1.00 0.00 H ATOM 2 O5' C A 1 -30.685 -20.928 3.695 1.00 0.00 O ATOM 3 C5' C A 1 -30.499 -22.286 3.303 1.00 0.00 C ATOM 4 H5' C A 1 -30.674 -22.932 4.190 1.00 0.00 H ATOM 5 H5'' C A 1 -29.451 -22.408 2.957 1.00 0.00 H ATOM 6 C4' C A 1 -31.442 -22.699 2.192 1.00 0.00 C ATOM 7 H4' C A 1 -31.693 -23.777 2.284 1.00 0.00 H ATOM 8 O4' C A 1 -32.682 -21.940 2.275 1.00 0.00 O ATOM 9 C1' C A 1 -33.141 -21.611 0.975 1.00 0.00 C ATOM 10 H1' C A 1 -34.185 -21.975 0.869 1.00 0.00 H Any help or suggestions? Newlyn Joseph, M.S. M.D. Candidate, Class of 2023 University of Connecticut School of Medicine nejos...@uchc.edu | new.josep...@gmail.com (203) 584-6402 sent from Outlook Web App
-- ================================================== 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.
