Error during "Building Normal Complex Amber topology"

[Saurabh Sharma]

Hello,

I am running gmx_MMPBSA with the following command:

`gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct md_0_10.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv`

The command ends with error:

`File "/home/saurabh/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/topologyobjects.py", line 931, in exclude
    raise MoleculeError("Cannot exclude an atom from itself! "
MoleculeError: Cannot exclude an atom from itself! Atoms are: <Atom CL [0]; In UNK 0> <Atom CL [0]; In UNK 0>
Exiting. All files have been retained.
`

I would really appreciate any help with this.

Thank you

[marioe911116]

There is an issue with the topology... could you please send us the prm and the itp for the molecule UNK?

[Saurabh Sharma]

Hello,

I have attached the relevant files.

Thank you.

[marioe911116]

I see the ligand contains an LPH particle... please follow this tutorial https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff/

[Saurabh Sharma]

Thank you for the great help. The tutorial addresses my use case. However, I have trouble generating the right index file and making the right correction n the 'topol.top' file. Specifically, I have the following confusions:

In the example, the LPH atom is at position 47-48. In my case it is only at position 54. So I went with the following options, without completely understanding what they do, but changing them as per my use case.

Grouping both LPH particles

 >54

Excluding both LPH particles from the ligand

>13&!55

Naming ligand as lig

>name 50 lig

Grouping rec and lig

>1|56

Cleaning

>del 17-55

Ran it with:

> gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 13 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

Ended up with:

> MMPBSA_Error: /usr/local/gromacs/bin/gmx make_ndx failed when querying index_mod_gromacs.ndx

[Mario Ernesto]

Can you send the files... That way it is going to be easier to address the error 

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[Saurabh Sharma]

Thank you for helping. I have attached more files. BTW, if I try running gmx_MMPBSA by not changing anything apart from the content of mmpbsa.in to the following, the analysis starts running but doesn't complete even after hours:

```
&general
sys_name="PB_Halogens",
PBRadii=7,
/
&pb
inp=1, radiopt=0, cavity_surften=0.005, cavity_offset=0.0000
/

```

Thank you,

Saurabh

[Mario Ernesto]

can you send the .tpr you are using?

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[Saurabh Sharma]

The tpr file I am using has been attached here. For some reason, it is being deleted from here.

[Mario Ernesto]

Could you please convert this into a pdb... I don't have the gromacs 2023...sorry for the inconvenience 

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