# Error with pdb2gmx when peptide is capped with N-terminal acetyl group **URL:** \ **Category:** User discussions\ **Created:** [July 21, 2021, 3:36pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped-with-n-terminal-acetyl-group/2556 "2021-07-21T15:36:40Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![alicepettitt](https://avatars.discourse-cdn.com/v4/letter/a/dbc845/32.png) [@alicepettitt](https://gromacs.bioexcel.eu/u/alicepettitt)\ **Post date:** [July 21, 2021, 3:36pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped-with-n-terminal-acetyl-group/2556/1 "2021-07-21T15:36:40Z")
GROMACS version: 2021.2 GROMACS modification: No I am trying to produce a .gro file using the charmm36m ff. My peptide is 21 residues long and has an acetyl group at the N-terminus. When I ran **gmx pdb2gmx -f peptide\_charmm.pdb -o peptide.gro -ignh -ter** I got the following error: **Residue 2 named ACE 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.** The atom names for ACE in the .rtp file are as follows: [ACE] ; N-terminal acetyl patch [atoms] CAY CT3 -0.270 1 HY1 HA3 0.090 1 HY2 HA3 0.090 1 HY3 HA3 0.090 1 CY C 0.510 2 OY O -0.510 2 and in my pdb file the ACE and first residue SER are shown below: ATOM 1 CAY ACE P 1 -2.160 -0.094 1.070 1.00 0.00 PROA ATOM 2 HY1 ACE P 1 -2.594 -0.183 2.088 1.00 0.00 PROA ATOM 3 HY2 ACE P 1 -2.503 -0.953 0.455 1.00 0.00 PROA ATOM 4 HY3 ACE P 1 -2.503 0.860 0.614 1.00 0.00 PROA ATOM 5 CY ACE P 1 -0.672 -0.102 1.160 1.00 0.00 PROA ATOM 6 OY ACE P 1 -0.105 -0.197 2.247 1.00 0.00 PROA ATOM 7 N SER P 2 0.000 0.000 0.000 1.00 0.00 PROA ATOM 8 HN SER P 2 -0.453 0.078 -0.885 1.00 0.00 PROA ATOM 9 CA SER P 2 1.461 0.000 0.000 1.00 0.00 PROA ATOM 10 HA SER P 2 1.786 -0.916 -0.471 1.00 0.00 PROA ATOM 11 CB SER P 2 2.051 1.206 -0.743 1.00 0.00 PROA ATOM 12 HB1 SER P 2 1.854 2.133 -0.163 1.00 0.00 PROA ATOM 13 HB2 SER P 2 1.581 1.291 -1.746 1.00 0.00 PROA ATOM 14 OG SER P 2 3.466 1.063 -0.911 1.00 0.00 PROA ATOM 15 HG1 SER P 2 3.758 1.849 -1.379 1.00 0.00 PROA ATOM 16 C SER P 2 1.915 0.000 1.471 1.00 0.00 PROA ATOM 17 O SER P 2 1.128 0.000 2.417 1.00 0.00 PROA I would be really grateful if anyone could offer advice on how to overcome this error. Thank you in advance! ---
**Author:** ![slovas](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@slovas](https://gromacs.bioexcel.eu/u/slovas)\ **Post date:** [July 21, 2021, 5:31pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped-with-n-terminal-acetyl-group/2556/2 "2021-07-21T17:31:33Z")
I had the same problem, and eventually I have changed the ACE in the merged.rtp using the older definition of the atom names in ACE: [atoms] CH3 CT3 -0.270 1 HH31 HA3 0.090 1 HH32 HA3 0.090 1 HH33 HA3 0.090 1 C C 0.510 2 O O -0.510 2 [bonds] C CH3 C +N CH3 HH31 CH3 HH32 CH3 HH33 O C [impropers] C CH3 +N O Bests, Sandor ---
**Author:** ![alicepettitt](https://avatars.discourse-cdn.com/v4/letter/a/dbc845/32.png) [@alicepettitt](https://gromacs.bioexcel.eu/u/alicepettitt)\ **Post date:** [July 22, 2021, 9:11am UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped-with-n-terminal-acetyl-group/2556/3 "2021-07-22T09:11:05Z")
Hi Sandor, Thank you so much for the advice. It worked for me too :) I really appreciate your help! Best wishes, Alice