Running gmx_MMPBSA with the Latest GROMACS 2026 Version (Workaround Guide)

[marioe911116]

This mini-tutorial describes a practical workaround to run gmx_MMPBSA with the latest version of GROMACS (2026), which has not been fully tested in the gmx_MMPBSA environment. We plan to implement this to be performed automatically in future versions of gmxMMPBSA.


The workflow consists of three main steps:

1. Define the path to the desired GROMACS executable in mmpbsa.in
2. Convert relative force field paths in the topology to absolute paths
3. Remove or comment CMAP terms in topology files

### 1. Define the GROMACS Path in mmpbsa.in

If the latest GROMACS version is installed in a separate conda environment (or custom location), gmx_MMPBSA may not automatically detect it. Therefore, you must explicitly define the path to the GROMACS binary directory inside the &general namelist of the mmpbsa.in file.

The path should point to the directory containing the gmx executable.

```
Sample input file for PB calculation
This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended in the
Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time.
Feel free to change the parameters according to what is better for your system.

&general
sys_name="Linear_PB",
startframe=1,
endframe=10,
gmx_path="/home/mario/miniconda3/envs/gromacs_2026/bin.AVX2_256"
/
&pb
radiopt=0, istrng=0.150,
/
```

#### Notes

- gmx_path must point to the folder containing the gmx executable.
- Do not include /gmx at the end of the path.
- Verify correctness by running: `/path/to/bin.AVX2_256/gmx --version`

### 2. Convert Relative Force Field Paths to Absolute Paths

gmx_MMPBSA may fail if topology files reference force field files using relative paths. To avoid path resolution issues, convert all force field includes to absolute paths.

Original Topology (com.top)

```
; Include forcefield parameters
#include "amber19sb.ff/forcefield.itp"

; Include water topology
#include "amber19sb.ff/opc3.itp"

; Include topology for ions
#include "amber19sb.ff/ions_opc3.itp"
```

Modified Topology with Absolute Paths

```
; Include forcefield parameters
#include "/home/mario/miniconda3/envs/gromacs_2026/share/gromacs/top/amber19sb.ff/forcefield.itp"

; Include water topology
#include "/home/mario/miniconda3/envs/gromacs_2026/share/gromacs/top/amber19sb.ff/opc3.itp"

; Include topology for ions
#include "/home/mario/miniconda3/envs/gromacs_2026/share/gromacs/top/amber19sb.ff/ions_opc3.itp"
```

#### Important

- Only force field includes require absolute paths.
- System-specific files (e.g., com_Protein_chain_A.itp) can remain relative if located in the working directory.
- Ensure consistency across .top and .itp files.

### 3. Comment Out CMAP Sections

gmx_MMPBSA currently does not support CMAP corrections in the newest GROMACS 2026 amber19sb and amber14sb force field ports. If present, they must be removed or commented out in both .top and .itp files. This will not affect the final results since these terms cancel out after taking the difference DG=COM-REC-LIG. CMAP blocks are usually located toward the end of topology files and look like this:

```
[ cmap ]
;  ai    aj    ak    al    am funct            c0            c1
    8    10    12    19    21     1
   19    21    23    33    35     1
   33    35    37    43    45     1
   43    45    55    57    59     1
   57    59    69    71    73     1
   71    73    75    90    92     1
   90    92   102   104   106     1
```

Corrected Version (Commented Out)

Add ; at the beginning of each line:

```
;[ cmap ]
;;  ai    aj    ak    al    am funct            c0            c1
;    8    10    12    19    21     1
;   19    21    23    33    35     1
;   33    35    37    43    45     1
;   43    45    55    57    59     1
;   57    59    69    71    73     1
;   71    73    75    90    92     1
;   90    92   102   104   106     1
```

#### Key Points
- Apply this modification to all topology-related files where [ cmap ] appears.
- Failing to remove CMAP terms will typically result in parsing errors during the MMPBSA setup phase.
- Do not modify other dihedral or bonded terms.

After completing these steps, gmx_MMPBSA should correctly use the latest installed GROMACS version for energy calculations.

This workaround allows compatibility without modifying the internal gmx_MMPBSA environment. We plan to implement this automatically in future versions of gmxMMPBSA.