# Rtp conversion charmm36 **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx\ **Created:** [July 5, 2022, 7:50pm UTC](https://gromacs.bioexcel.eu/t/rtp-conversion-charmm36/4415 "2022-07-05T19:50:19Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 5, 2022, 7:50pm UTC](https://gromacs.bioexcel.eu/t/rtp-conversion-charmm36/4415/1 "2022-07-05T19:50:19Z")
GROMACS version:2022 GROMACS modification:No Hello all, I am having trouble converting my modified residue to rtp format. I methylated my residue ```auto ATOM 781 N ARG A 130 8.714 54.987 2.676 1.00 47.63 N ATOM 782 CA ARG A 130 9.061 56.391 2.868 1.00 47.63 C ATOM 783 C ARG A 130 9.052 57.092 1.516 1.00 47.63 C ATOM 784 O ARG A 130 8.614 58.234 1.401 1.00 47.63 O ATOM 785 CB ARG A 130 10.437 56.528 3.519 1.00 76.92 C ATOM 786 CG ARG A 130 10.508 55.943 4.915 1.00 76.92 C ATOM 787 CD ARG A 130 11.825 56.267 5.593 1.00 76.92 C ATOM 788 NE ARG A 130 11.900 55.657 6.916 1.00 76.92 N ATOM 789 CZ ARG A 130 12.901 55.838 7.770 1.00 76.92 C ATOM 790 NH1 ARG A 130 13.923 56.618 7.443 1.00 76.92 N1+ ATOM 791 NH2 ARG A 130 12.882 55.239 8.953 1.00 76.92 N ATOM 792 C01 ARG A 130 13.991 55.440 9.897 0.00 0.00 C ATOM 793 C02 ARG A 130 11.752 54.374 9.321 0.00 0.00 C ATOM 794 H02 ARG A 130 14.312 54.511 10.265 0.00 0.00 H ATOM 795 H05 ARG A 130 11.340 54.701 10.229 0.00 0.00 H ATOM 796 H03 ARG A 130 13.667 56.040 10.695 0.00 0.00 H ATOM 797 H06 ARG A 130 12.088 53.384 9.424 0.00 0.00 H ATOM 798 H04 ARG A 130 14.787 55.915 9.404 0.00 0.00 H ATOM 799 H07 ARG A 130 11.020 54.417 8.569 0.00 0.00 H ``` then used cgenff to generate a itp to convert to an rtp ```auto ; Atom type charge O2 OG2D1 -0.548 1 ;carbonyl O N NH1 -0.4700 2 ;peptide nitrogen N2 NG2D1 -0.824 3 ;N for neutral imine/Schiff's base C=N-R N3 NG301 -0.137 4 ;neutral trimethylamine nitrogen N4 NG321 -0.502 5 ;neutral methylamine C1 CG321 -0.281 6 ;C for CH2 C3 CG321 -0.196 7 ;C for CH2 C4 CG311 0.326 8 ;ch C5 CG321 0.015 9 ;C for CH2 C2 CG2O2 0.779 10 ;carbonyl C peptide backbone C6 CG2N1 0.500 11 ;conjugated C in guanidine C7 CG331 -0.207 12 ;C for methyl group CH3 C8 CG331 -0.207 13 ;C for methyl group CH3 H1 HGA2 0.090 14 ;alphatic proton, CH2 H2 HGA2 0.090 15 ;alphatic proton, CH2 H3 HGA2 0.090 16 ;alphatic proton, CH2 H4 HGA2 0.090 17 ;alphatic proton, CH2 H5 HGA1 0.090 18 ;alphatic proton, CH H6 HGA2 0.090 19 ;alphatic proton, CH2 H7 HGA2 0.090 20 ;alphatic proton, CH2 H10 HGA3 0.090 23 ;alphatic proton, CH3 H11 HGA3 0.090 24 ;alphatic proton, CH3 H12 HGA3 0.090 25 ;alphatic proton, CH3 H13 HGA3 0.090 26 ;alphatic proton, CH3 H14 HGA3 0.090 27 ;alphatic proton, CH3 H15 HGA3 0.090 28 ;alphatic proton, CH3 ``` Because I have to add hydrogens for cgenff and the atom names dont carry over I have lost track of my hydrogens. Can someone help me with the error when I use pdb2gmx ```auto Fatal error: Atom N in residue AMA 130 was not found in rtp entry AMA with 32 atoms while sorting atoms. . ``` is there a way to label files when switiching formats from pdb to mol2 to str to itp since I have tried to label my mol2 and rtp could someone tell me why there is an error in applying my rtp to my pdb? rtp ```auto ; Name [AMA] [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB N1 NG321 -1.081 ;neutral methylamine C1 CG311 0.369 ;ch C2 CG2O4 0.142 ;carbonyl C aldehyde O1 OG2D1 -0.389 ;carbonyl O C3 CG321 -0.196 ;C for CH2 C4 CG321 -0.196 ;C for CH2 C5 CG321 0.015 ;C for CH2 N2 NG2D1 -0.824 ;N for neutral imine/Schiff's base C=N-R C6 CG2N1 0.500 ;conjugated C in guanidine N3 NG321 -0.502 ;neutral methylamine N4 NG301 -0.137 ;neutral trimethylamine nitrogen C7 CG331 -0.207 ;C for methyl group CH3 C8 CG331 -0.207 ;C for methyl group CH3 H1 HGA3 0.090 ;alphatic proton, CH3 H2 HGA3 0.090 ;alphatic proton, CH3 H3 HGA3 0.090 ;alphatic proton, CH3 H4 HGA3 0.090 ;alphatic proton, CH3 H5 HGA3 0.090 ;alphatic proton, CH3 H6 HGA3 0.090 ;alphatic proton, CH3 H7 HGA2 0.090 ;alphatic proton, CH2 H8 HGA2 0.090 ;alphatic proton, CH2 H9 HGPAM2 0.330 ;polar H, NEUTRAL methylamine H10 HGA2 0.090 ;alphatic proton, CH2 H11 HGA2 0.090 ;alphatic proton, CH2 H12 HGPAM2 0.330 ;polar H, NEUTRAL methylamine H13 HGA2 0.090 ;alphatic proton, CH2 H14 HGA2 0.090 ;alphatic proton, CH2 H15 HGPAM2 0.396 ;polar H, NEUTRAL methylamine H16 HGPAM2 0.396 ;polar H, NEUTRAL methylamine H17 HGA1 0.090 ;alphatic proton, CH H18 HGR52 0.091 ; Aldehyde H, formamide H (RCOH ``` pdb ```auto ATOM 781 N1 AMA A 130 8.714 54.987 2.676 1.00 47.63 N ATOM 782 C1 AMA A 130 9.061 56.391 2.868 1.00 47.63 C ATOM 783 C2 AMA A 130 9.052 57.092 1.516 1.00 47.63 C ATOM 784 O1 AMA A 130 8.614 58.234 1.401 1.00 47.63 O ATOM 785 C3 AMA A 130 10.437 56.528 3.519 1.00 76.92 C ATOM 786 C4 AMA A 130 10.508 55.943 4.915 1.00 76.92 C ATOM 787 C5 AMA A 130 11.825 56.267 5.593 1.00 76.92 C ATOM 788 N2 AMA A 130 11.900 55.657 6.916 1.00 76.92 N ATOM 789 C6 AMA A 130 12.901 55.838 7.770 1.00 76.92 C ATOM 790 N3 AMA A 130 13.923 56.618 7.443 1.00 76.92 N1+ ATOM 791 N4 AMA A 130 12.882 55.239 8.953 1.00 76.92 N ATOM 792 C7 AMA A 130 13.991 55.440 9.897 0.00 0.00 C ATOM 793 C8 AMA A 130 11.752 54.374 9.321 0.00 0.00 C ATOM 794 H1 AMA A 130 14.312 54.511 10.265 0.00 0.00 H ATOM 795 H2 AMA A 130 11.340 54.701 10.229 0.00 0.00 H ATOM 796 H3 AMA A 130 13.667 56.040 10.695 0.00 0.00 H ATOM 797 H4 AMA A 130 12.088 53.384 9.424 0.00 0.00 H ATOM 798 H4 AMA A 130 14.787 55.915 9.404 0.00 0.00 H ATOM 799 H7 AMA A 130 11.020 54.417 8.569 0.00 0.00 H ``` ```auto Fatal error: Residue 100 named AMA of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ``` ---
**Author:** ![ddesh5208660](https://avatars.discourse-cdn.com/v4/letter/d/8797f3/32.png) [@ddesh5208660](https://gromacs.bioexcel.eu/u/ddesh5208660)\ **Post date:** [November 17, 2023, 5:18am UTC](https://gromacs.bioexcel.eu/t/rtp-conversion-charmm36/4415/2 "2023-11-17T05:18:41Z")
Try adding [bond] in rtp file to keep track of your hydrogen. This should fix then.