Pdb2gmx doesn't recognize ASPH residue

User discussions
1

GROMACS version: gmx, version 2022.2
GROMACS modification: No

I am trying to use protonated ASP residue ASPH which is already defined in my aminoacids.rtp and residuetypes.dat in my forcefield and even default within the GROMACS top folder. I believe the pdb is formated correctly:

ATOM   2357  C   ALA P 148     -12.697 -21.325 -26.411  1.00  0.00      PROA
ATOM   2358  O   ALA P 148     -12.796 -21.972 -25.340  1.00  0.00      PROA
ATOM   2359  N   ASPHP 149     -13.187 -21.748 -27.571  1.00  0.00      PROA
ATOM   2360  HN  ASPHP 149     -12.903 -21.351 -28.440  1.00  0.00      PROA
ATOM   2361  CA  ASPHP 149     -14.194 -22.844 -27.651  1.00  0.00      PROA
ATOM   2362  HA  ASPHP 149     -14.291 -23.274 -26.665  1.00  0.00      PROA
ATOM   2363  CB  ASPHP 149     -15.557 -22.331 -28.138  1.00  0.00      PROA
ATOM   2364  HB1 ASPHP 149     -16.111 -21.924 -27.266  1.00  0.00      PROA
ATOM   2365  HB1 ASPHP 149     -16.122 -23.187 -28.563  1.00  0.00      PROA
ATOM   2366  CG  ASPHP 149     -15.488 -21.245 -29.196  1.00  0.00      PROA
ATOM   2367  OD1 ASPHP 149     -14.414 -21.098 -29.820  1.00  0.00      PROA
ATOM   2368  OD2 ASPHP 149     -16.504 -20.524 -29.361  1.00  0.00      PROA
ATOM   2369  HD2 ASPHP 149     -16.418 -19.850 -30.039  1.00  0.00      PROA
ATOM   2370  C   ASPHP 149     -13.688 -23.982 -28.536  1.00  0.00      PROA
ATOM   2371  O   ASPHP 149     -14.543 -24.689 -29.073  1.00  0.00      PROA
ATOM   2372  N   PHE P 150     -12.374 -24.198 -28.657  1.00  0.00      PROA
ATOM   2373  HN  PHE P 150     -11.691 -23.590 -28.259  1.00  0.00      PROA

However pdb2gmx doesn’t think it’s an ASPH residue. It still thinks it’s an ASP residue:

Fatal error:
Atom HD2 in residue ASP 149 was not found in rtp entry ASP with 12 atoms
while sorting atoms.
2

I guess this isn’t done automatically by pdb2gmx? According to most up to date version/bug fixes you need to enter this manually with -asp flag and select for each aspartic individually.

Protonated forms are only available via the interactive selection options