Wrong residue chain in decomposition analysis

[Muhamad Alif Bin Che Nordin]

Hi guys!

For context:

I am running &gb and &decomp analysis onto a trajectory of 4,556 frames between 3 chains (Receptor: A,B and Ligand:C). I have defined two groups as my index file (Receptor: A,B and Ligand:C) but somehow gmxMMPBSA has selected residues decomposition analysis (Receptor: A,B and C and Ligand:C).

It seemed that gmxMMPBSA has included chain C in the receptor. I think i have properly defined my atoms in my index file, but i might be wrong. i dont know.

I dont have the entire output files as the calculation is still on-going. Should i wait for the analysis to complete or should i stop and redo?

[marioe911116]

I can't tell if the residues in the index files are correct or not at least I have the files... if you send us the files I can take a look

[Mario Sergio Valdes]

For decomposition, at least one residue of the receptor and the ligand is required. In this case, no matter how many chains the receptor or ligand has, they will be extracted as long as the distance criterion is met. If you defined the residue selection for decomposition automatically, gmx_MMPBSA will extract all residues of the receptor and ligand that are within 6 A of each other.
The definition of the C chain in the output appears as R:C:XXX:xxx or L:C:XXX:xxx? Please show us the terminal output

[Muhamad Alif Bin Che Nordin]

Thank you marioe911116 & Mario Sergio Valdes,

The files (in a single zip file) can be accessed thru this link. 

The chains are written as follows:

R:A:TYR:56
R:B:ARG:30
R:C:ALA:36
L:C:SER:132

However, there's no overlap of chain C residues in R and L. gmxMMPSBA identified the 6A residues for chain C (R between residues 36-131 while L between residues 132-332).

Log file is as attached.

Thanks

[Mario Sergio Valdes]

Please double-check that you have generated the groups correctly. The receptor has a fragment of the chain C up to residue 131, while the ligand extends from chain C residue 132.