Calculating binding energy for Multiple PDBs

PRODIGY
1

Dear Sir/Madam,
I would like to compute the binding free energy for multiple PDBs. How could I do it with your program. Please do help me out.

2

Hi,

You just need to compress the directory containing all the files you want to analyse ans submit it. Please notice, through the server you can also do it with pdb structures that has the same chain identifiers, since it is only possible to provide this command once.

Best regards,
Anna

3

Dear Anna,
I tried submitting the ZIP file in the web server for the calculation and ended with the error stating “Error during parsing the input structure: File exceeds allowed size limit of 10 MB”. On the other hand, I also tried using the command line with the command python predict_IC.py test.zip --selection A C

output error:
[+] Reading structure file: /home/rajasekaran/Documents/prodigy-master/test.zip
Traceback (most recent call last):
File “predict_IC.py”, line 284, in
structure, n_chains, n_res = parse_structure(struct_path)
File “/home/rajasekaran/Documents/prodigy-master/lib/parsers.py”, line 117, in parse_structure
raise IOError(’[!] Structure format ‘{0}’ is not supported. Use ‘.pdb’ or ‘.cif’.’.format(s_ext))
IOError: [!] Structure format ‘zip’ is not supported. Use ‘.pdb’ or ‘.cif’.

Please do help me out with the error.

with regards
Srinivasan

4

Hi,

we might increase the size limit of the server. For now you can try to split your PDB files into multiple archives smaller then 10 mb and submit several runs.
For the command line you will have to call the script with a simple loop multiple times e.g in bash:
for pdb in *pdb; do python predict_IC.py $pdb --selection A C; done

Regards,

Joerg

5

Thank you very much Anna.

with regards,
Srinivasan