receptor preparation with membrane

[aashuph16221]

Hello,

I am working with a membrane protein and would like to include POPC to account for boundary effects during docking. Without POPC, I am able to use the docking command successfully. However, when I include POPC, I am unable to generate the PDBQT file.

Is there a way to incorporate POPC with protein into the PDBQT file as well?

Regards,

Aashish

[diogomart]

Hi, I'd expect it to work as long as the POPC residue is named POV, to download the correct template from the chemical component dictionary. What error are you getting?

[aashuph16221]

Hi @diogomart

Earlier, I got an error saying "there is no residue POP".
I changed the name from POPC to POV, and now it works.

I have one query. When I used
mk_prepare_receptor.py -i pro.pdb -o pro.pdbqt

it stopped and displayed the message:
"Use -o/--output_basename, or set a filename after each --write flag"

then i used the command:

mk_prepare_receptor.py -i pro.pdb --write_pdbqt pro.pdbqt

it worked perfectly.

So is this method correct, or did I just force the command to generate the PDBQT file?

Apart from that, is there any other way to check which non-standard residues mk_prepare_receptor.py can process?

Thanks for the help.

[diogomart]

The -o is for setting an output basename, and then multiple output files will be written with different extensions. For example:

-o rec -j -p -g

is equivalent to

-j rec.json -p rec.pdbqt -g rec.gpf

It can process anything it downloads from the chemical component dictionary except if there are covalent bonds to other residues. For example: glycans, or heme where iron is coordinated by a cysteine.

[aashuph16221]

The reason I asked is because when I used POPC, I got the following error:

---

No template matched for residue_key='J:645'
tried 1 templates for residue_key='J:645'excess_H_ok=False
POP heavy_miss=4 heavy_excess=47 H_excess=[] bond_miss=set() bond_excess=set()

However, when I renamed it to POV, it worked.
So if I want to check whether a residue name will be recognized by meeko, is there a way to verify which residue names it can process?

For example, if I want to use cholesterol or any other lipid that is already available in the chemical component dictionary, how can I check whether meeko supports it?

[diogomart]

If any residue isn't recognized and option --allow_bad_res or -a is not used, meeko throws an error and doesn't write output files. When--allow_bad_res or -a is used, unrecognized or unmatched residues are removed from the output files. If you did not use -a / --allow_bad_res then all residues in the input file were successfully matched against templates.