Questions about the file needed for CDOCKER

[hima111997]

Hi

I was trying CDOCKER after i have moved most of the necessary files (parameters, topology, pdb and psf files) from the repo to another folder then i used the following code to perform the docking:

import os
os.chdir('/content/trial')
os.environ['CHARMM_LIB_DIR'] = '/content/drive/MyDrive/PyCharmm/charmm/build_charmm/lib'
## Import module
import numpy as np
import pycharmm
import pycharmm.lib as lib
import pycharmm.read as read
import pycharmm.lingo as lingo
import pycharmm.settings as settings
from pycharmm.cdocker import Rigid_CDOCKER

################################################################
# #
# #     Begin of pyCHARMM Rigid CDOCKER
# #
# ###############################################################

## Topology and parameter files
settings.set_bomb_level(-1)

read.rtf('"./top_all36_prot.rtf"')
read.rtf('"./top_all36_cgenff.rtf"', append = True)
read.prm('"./par_all36m_prot.prm"', flex = True)
read.prm('"./par_all36_cgenff.prm"', append = True, flex = True)
settings.set_bomb_level(0)
read.stream('ligandrtf')

## Import module
from pycharmm.cdocker import Rigid_CDOCKER

## File name and pathway
ligPDB = "ligand.pdb"
ligandrtf = "ligandrtf"
confDir = "/content/conformer/"
receptorPDB = "protein.pdb"
receptorPSF = "protein.psf"

## Rigid CDOCKER standard docking protocol
clusterResult, dockResult = Rigid_CDOCKER(xcen = 12.33, ycen = 33.48, zcen = 19.70,
                                        maxlen = 25.762, ligPDB = ligPDB, receptorPDB = receptorPDB,
                                        receptorPSF = receptorPSF, confDir = confDir, flag_grid = False,
                                        flag_delete_conformer = False, numPlace = 5)

print(clusterResult)
print(dockResult)

However, this produced an error regarding the probe file, as it could not find it. 1- Is it correct to use the provided probe file when performing docking using other proteins and ligands? i have read this paper (Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms) and it mentioned that there are 26 grids used which are generated using the values in the probe file.

2- for the fftdock_rotation_1.qua file, I noticed that the code found in the supplementary file of the previous paper used this file. So is it correct to use the provided file or do i need to generate another one and how to generate it?

3- regarding question 2, when i moved the probe file to the new working directory (without the fftdock_rotation_1 file) and changed the default directory in Rigid_CDOCKER, the docking completed without an error. So, does this mean that the docking does not need this file?

edit: i noticed that this line contained an exclamation mark at the beginning (! open unit 40 read form name @0/fftdock_rotation_1.qua), so it is a comment

Thanks