# Pdb2gmx doesn't recognize ASPH residue

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-doesnt-recognize-asph-residue/5520>\
**Category:** User discussions\
**Created:** [January 3, 2023, 7:10am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-doesnt-recognize-asph-residue/5520 "2023-01-03T07:10:34Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![bjwiley23](https://avatars.discourse-cdn.com/v4/letter/b/c6cbf5/32.png) [@bjwiley23](https://gromacs.bioexcel.eu/u/bjwiley23)\
**Post date:** [January 3, 2023, 7:10am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-doesnt-recognize-asph-residue/5520/1 "2023-01-03T07:10:34Z")

</div>

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:

```auto
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:

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

```

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<div class="post-metadata">

**Author:** ![bjwiley23](https://avatars.discourse-cdn.com/v4/letter/b/c6cbf5/32.png) [@bjwiley23](https://gromacs.bioexcel.eu/u/bjwiley23)\
**Post date:** [January 3, 2023, 7:29am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-doesnt-recognize-asph-residue/5520/2 "2023-01-03T07:29:16Z")

</div>

I guess this isn’t done automatically by pdb2gmx? According to most [up to date version/bug fixes](https://manual.gromacs.org/current/release-notes/2021/major/bugs-fixed.html#pdb2gmx-handles-asph-and-gluh-inputs-better) 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_