interaction energy using foldx to calculate stability

Question

[sba5k]

Hello,

I am currently trying to find the stability of a protein (∆∆G) using foldx. I have a pdb of 3L6P (https://www.rcsb.org/structure/3L6P). I want to find the stability of this protein and compare it to a mutated version of 3L6P (not necessarily by using foldx), however, I am stumped. I am getting an error with foldx saying

"Sorry there is only one molecule in the PDB, we cannot calculate the interaction energy
There was a problem with the complex analysis of ./3l6p.pdb"

I was wondering if anyone could help me either find a way around this issue or give me some insight on how someone should go about calculating the stability of a protein.

[MSRS]

Can you please give the steps which you followed in foldX? You can also try dynamut.

[sba5k]

The link at the bottom will download the commands I found on pcbi with a small explanation . Otherwise it is these three

>foldx --command=RepairPdb --pdb=pdbFile.pdb

>foldx --pdb=pdbRepired.pdb --command=BuildModel --mutant-file=individual_list.txt

>foldx --pdb=BuildModelOutputFile.pdb --command=AnalyseComplex -- analyseComplexChains=A,E --pdbWaters=true --water=-PREDICT

I will also try out dynamut and let you know if that works.

Link to foldx commands

Answer 1

[MSRS]

foldx --pdb=BuildModelOutputFile.pdb --command=AnalyseComplex -- analyseComplexChains=A,E --pdbWaters=true --water=-PREDICT

Please, check analyseComplexChain, check the pdb file. I think there is only one chain ( Chain A) in the pdb file you used.

You can use foldX in YASARA plague in on Windows OS. I have an excellent experience on that.

[sba5k]

Yes, you are correct about only one chain in the pdb file. Would it not be possible to calculate the ∆∆G of that pdb then. Would dynamut be able to calculate the stability of that protein even if it is a single chain? I will also try out YASARA.

[MSRS]

Yes, dymamut can calculate it.

Please accept the answer if you find it helpful.

Thanks

[sba5k]

Thank you very much dynamut was very helpful!