[gmx-users] Gromacs-5.1.4 with CHARMM36 March 2019 RNA Residue Fatal Error

[Justin Lemkul]

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
> nejoseph at uchc.edu | new.joseph10 at 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
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jalemkul at vt.edu | (540) 231-3129
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