Open FeiLiuEM opened 1 year ago
@atillack @L30nardoSV @scottlegrand
please ( •᷄人•᷅ )
@FeiLiuEM could you post the contents of the .gpf
file?
@diogomart Here is the .gpf
file:
npts 24 22 32 # num.grid points in xyz
gridfld 1stp_receptor.maps.fld # grid_data_file
spacing 0.375 # spacing(A)
receptor_types A C NA OA N SA HD # receptor atom types
ligand_types A C OA N SA HD # ligand atom types
receptor 1stp_receptor.pdbqt # macromolecule
gridcenter 10.734 2.033 -11.537 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map 1stp_receptor.A.map # atom-specific affinity map
map 1stp_receptor.C.map # atom-specific affinity map
map 1stp_receptor.OA.map # atom-specific affinity map
map 1stp_receptor.N.map # atom-specific affinity map
map 1stp_receptor.SA.map # atom-specific affinity map
map 1stp_receptor.HD.map # atom-specific affinity map
elecmap 1stp_receptor.e.map # electrostatic potential map
dsolvmap 1stp_receptor.d.map # desolvation potential map
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant
And this is the .gpf
file from the original example which is mainly different:
receptor_types A C H HD N OA # receptor atom types
ligand_types A C OA N SA HD # ligand atom types
@diogomart Oh, I find the problem.
I forget to delete drug in pdb
file. This is my fault.
I still want to know if there is a recommended method for prepare receptor. Thanks!
We are working on receptor preparation. There's a recently developed and feature-incomplete mk_prepare_receptor.py
in meeko, currently in branch "reactive" but should be released as v0.5.0 soon. This script strictly requires residue and atom names following the Amber naming scheme, so the input PDB must have been massaged by some Amber compliant tool (wk_prepare_receptor.py
from waterkit). The other option is the script you are already using, either from MGLTools or from ADFR/AGFR as described in the Vina docs.
Thanks a million! @diogomart diogomart
Looking forward to the meeko v0.5.0 release.
Thanks!
Hello,
I have a problem of preparing receptor and ligand.
Take 1stp for example. The preparation process is as follows:
The results are confusingly high:
I noticed that the
1stp_receptor.pdbqt
is very different from the example provided one and it influences the1stp_receptor.gpf
file.I want to ask 2 questions:
1stp_receptor.pdbqt
, which method is recommended for preparing receptor?