Error during "Mutating trajectories..." – Alanine Scanning

[Lara]

Hi,

I hope someone can help me with this problem: 

I have simulated protein-peptide complexes and now I want to perform Alanine Scanning for each residue of the 6 different peptides (16-17 residues). 

Everything worked fine except for the C-terminal residues (no caps).

I got the following error:

File "xxx/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj
    temp_holder.append(words[i])
IndexError: list index out of range

I noticed that this error occurred for TRP, LYS and ARG but not for HIS. Here, the program has changed the residue type from HIS to HIE, even though it is not protonated. Perhaps it was recognised as HIE because it has 1 more atom (not H but O at the C-terminus).

Could the additional O be the problem for all C-terminal residues?

However, it seems to be recognised by the program as a C-terminal O and is also stated as OXT in the output pdb files.

So why this index problem?

[Mario Sergio Valdes]

Hi Lara

Normally, we avoid mutating the terminals and the truth is that we have not tested it extensively. I will try to modify it ASAP so that you can use it in your work.

Mario S.