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4ieh_protein.glg
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_______________________________________________________
__________//____________________________/////_________________/________
_________/__/____________/_____________/______________/_______/________
________/____/___________/_____________/______________________/________
________/____/__/_____/_/////___/////__/__////_/_///__/__////_/________
_______/______/_/_____/__/_____/_____/_/_____/_//___/_/_/____//________
_______////////_/_____/__/_____/_____/_/_____/_/______/_/_____/________
_______/______/_/____//__/___/_/_____/_/_____/_/______/_/____//________
_______/______/__////_/___///___/////___/////__/______/__////_/________
_______________________________________________________
______
/ \
/ \
/ \
\ /\ /
\ / \ /
\/ /\ \/
/ \
/____\
______________________________________
| |
| AutoGrid 4.2.7.x.2019-09-11 |
| |
| Garrett M. Morris, TSRI |
| Ruth Huey, TSRI |
| David S. Goodsell, TSRI |
| Arthur J. Olson, TSRI |
| (MODIFIED VERSION DUAL HB) |
| |
| (C) 1989-2009, TSRI |
| The Scripps Research Institute |
|______________________________________|
______________________________________
| |
| Calculation of van der Waals, H-Bond,|
| Electrostatic Potential Energy, & |
| Desolvation Free Energy Grid Maps |
| for AutoDock |
| For help, email [email protected] |
|______________________________________|
$Revision: 1.145 $
Compilation parameters: NUM_RECEPTOR_TYPES=20 NEINT=2048
AG_MAX_ATOMS=100000 MAX_MAPS=128 NDIEL=16384 MAX_ATOM_TYPES=126
e_vdW_Hb table has 32514048 entries of size 8
Maximum number of maps that can be computed = 128 (defined by MAX_MAPS in "autocomm.h").
Non-bond cutoff for internal energy calculation (NBC): 8.00
Optimize internal energy scoring (USE_8A_NBCUTOFF): yes
Faster search for nearby atoms (USE_BHTREE): yes
Run calculations in parallel if possible (_OPENMP): no
This file was created at: 9:43 48" p.m., 02/24/2022
using: "Coffee-Lake"
GPF> npts 50 40 40 # num.grid points in xyz
Number of grid points in x-direction: 51
Number of grid points in y-direction: 41
Number of grid points in z-direction: 41
GPF> gridfld 4ieh_protein.maps.fld # grid_data_file
Creating (AVS-readable) grid maps file : 4ieh_protein.maps.fld
Creating (AVS-readable) grid-coordinates extrema file : 4ieh_protein.maps.xyz
GPF> spacing 0.375 # spacing(A)
Grid Spacing : 0.375 Angstrom
GPF> receptor_types A C OA N SA HD # receptor atom types
GPF> ligand_types A C Cl NA OA N S SA HD # ligand atom types
Allocated space for 12 gridmap objects
1 CPU thread will be used for calculation
Atom type names for ligand atom types 1-9 used for ligand-atom affinity grid maps:
Atom type number 0 corresponds to atom type name "A".
Atom type number 1 corresponds to atom type name "C".
Atom type number 2 corresponds to atom type name "Cl".
Atom type number 3 corresponds to atom type name "NA".
Atom type number 4 corresponds to atom type name "OA".
Atom type number 5 corresponds to atom type name "N".
Atom type number 6 corresponds to atom type name "S".
Atom type number 7 corresponds to atom type name "SA".
Atom type number 8 corresponds to atom type name "HD".
GPF> receptor 4ieh_protein.pdbqt # macromolecule
Receptor Input File : 4ieh_protein.pdbqt
Receptor Atom Type Assignments:
Maximum partial atomic charge found = +0.665 e
Minimum partial atomic charge found = -0.648 e
Atom Atom Number of this Type
Type ID in Receptor
____ ____ ___________________
0 A 151
1 C 592
2 OA 209
3 N 205
4 SA 6
5 HD 267
Total number of atoms : 1430 atoms
Total charge : -1.96 e
Receptor coordinates fit within the following volume:
_______(29.5, 39.6, 39.0)
/| /|
/ | / |
/______/ |
| |___|__| Midpoint = (6.0, 20.7, 19.7)
| / | /
| / | /
|/_____|/
(-17.4, 1.7, 0.5)
Maximum coordinates : (29.507, 39.635, 38.977)
Minimum coordinates : (-17.411, 1.739, 0.476)
GPF> gridcenter 12.303 25.141 11.066 # xyz-coordinates or auto
Grid maps will be centered on user-defined coordinates:
(12.303, 25.141, 11.066)
Grid maps will cover the following volume:
_______(21.7, 32.6, 18.6)
/| /|
/ | / |
/______/ |
| |___|__| Midpoint = (12.3, 25.1, 11.1)
| / | /
| / | /
|/_____|/
(2.9, 17.6, 3.6)
Grid map x-dimension : 18.8 Angstroms
Grid map y-dimension : 15.0 Angstroms
Grid map z-dimension : 15.0 Angstroms
Maximum coordinates : (21.678, 32.641, 18.566)
Minimum coordinates : (2.928, 17.641, 3.566)
GPF> smooth 0.5 # store minimum energy w/in rad(A)
Potentials will be smoothed by: 0.500 Angstrom
GPF> map 4ieh_protein.A.map # atom-specific affinity map
Output Grid Map 1: 4ieh_protein.A.map
GPF> map 4ieh_protein.C.map # atom-specific affinity map
Output Grid Map 2: 4ieh_protein.C.map
GPF> map 4ieh_protein.Cl.map # atom-specific affinity map
Output Grid Map 3: 4ieh_protein.Cl.map
GPF> map 4ieh_protein.NA.map # atom-specific affinity map
Output Grid Map 4: 4ieh_protein.NA.map
GPF> map 4ieh_protein.OA.map # atom-specific affinity map
Output Grid Map 5: 4ieh_protein.OA.map
GPF> map 4ieh_protein.N.map # atom-specific affinity map
Output Grid Map 6: 4ieh_protein.N.map
GPF> map 4ieh_protein.S.map # atom-specific affinity map
Output Grid Map 7: 4ieh_protein.S.map
GPF> map 4ieh_protein.SA.map # atom-specific affinity map
Output Grid Map 8: 4ieh_protein.SA.map
GPF> map 4ieh_protein.HD.map # atom-specific affinity map
Output Grid Map 9: 4ieh_protein.HD.map
GPF> elecmap 4ieh_protein.e.map # electrostatic potential map
Output Electrostatic Potential Energy Grid Map: 4ieh_protein.e.map
GPF> dsolvmap 4ieh_protein.d.map # desolvation potential map
Output Desolvation Free Energy Grid Map: 4ieh_protein.d.map
GPF> dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant
Using *distance-dependent* dielectric function of Mehler and Solmajer, Prot.Eng.4, 903-910.
>>> Closing the grid parameter file (GPF)... <<<
________________________________________________________________________________
Calculating Pairwise Interaction Energies
Beginning grid calculations.
Calculating 11 grids over 85731 elements, around 1430 receptor atoms.
Percent Estimated Time Time/this plane
XY-plane Z-coord Done Remaining Real, User, System
/Ang /sec /sec
________ ________ ________ ______________ __________________________
-20 3.566 2.4% 2.52s Real= 0.06, CPU= 0.06, System= 0.00
-19 3.941 4.9% 2.92s Real= 0.07, CPU= 0.08, System= 0.00
-18 4.316 7.3% 2.70s Real= 0.07, CPU= 0.06, System= 0.00
-17 4.691 9.8% 2.81s Real= 0.08, CPU= 0.08, System= 0.00
-16 5.066 12.2% 2.70s Real= 0.07, CPU= 0.08, System= 0.00
-15 5.441 14.6% 2.73s Real= 0.08, CPU= 0.08, System= 0.00
-14 5.816 17.1% 2.52s Real= 0.07, CPU= 0.08, System= 0.00
-13 6.191 19.5% 2.81s Real= 0.09, CPU= 0.08, System= 0.00
-12 6.566 22.0% 2.56s Real= 0.08, CPU= 0.08, System= 0.00
-11 6.941 24.4% 2.54s Real= 0.08, CPU= 0.09, System= 0.00
-10 7.316 26.8% 2.49s Real= 0.08, CPU= 0.08, System= 0.00
-9 7.691 29.3% 2.73s Real= 0.09, CPU= 0.09, System= 0.00
-8 8.066 31.7% 2.91s Real= 0.10, CPU= 0.11, System= 0.00
-7 8.441 34.1% 2.62s Real= 0.10, CPU= 0.09, System= 0.00
-6 8.816 36.6% 2.50s Real= 0.10, CPU= 0.09, System= 0.00
-5 9.191 39.0% 2.42s Real= 0.10, CPU= 0.09, System= 0.00
-4 9.566 41.5% 3.36s Real= 0.14, CPU= 0.12, System= 0.00
-3 9.941 43.9% 3.57s Real= 0.15, CPU= 0.12, System= 0.00
-2 10.316 46.3% 3.43s Real= 0.16, CPU= 0.16, System= 0.00
-1 10.691 48.8% 2.86s Real= 0.14, CPU= 0.12, System= 0.00
0 11.066 51.2% 2.80s Real= 0.14, CPU= 0.12, System= 0.00
1 11.441 53.7% 3.02s Real= 0.16, CPU= 0.16, System= 0.00
2 11.816 56.1% 2.52s Real= 0.14, CPU= 0.12, System= 0.02
3 12.191 58.5% 2.33s Real= 0.14, CPU= 0.14, System= 0.00
4 12.566 61.0% 2.51s Real= 0.16, CPU= 0.12, System= 0.00
5 12.941 63.4% 1.86s Real= 0.12, CPU= 0.12, System= 0.00
6 13.316 65.9% 2.14s Real= 0.15, CPU= 0.16, System= 0.00
7 13.691 68.3% 1.51s Real= 0.12, CPU= 0.11, System= 0.00
8 14.066 70.7% 1.57s Real= 0.13, CPU= 0.12, System= 0.00
9 14.441 73.2% 1.46s Real= 0.13, CPU= 0.12, System= 0.00
10 14.816 75.6% 1.46s Real= 0.15, CPU= 0.14, System= 0.00
11 15.191 78.0% 1.41s Real= 0.16, CPU= 0.16, System= 0.00
12 15.566 80.5% 1.16s Real= 0.14, CPU= 0.16, System= 0.00
13 15.941 82.9% 1.19s Real= 0.17, CPU= 0.14, System= 0.00
14 16.316 85.4% 0.90s Real= 0.15, CPU= 0.16, System= 0.00
15 16.691 87.8% 0.67s Real= 0.13, CPU= 0.14, System= 0.00
16 17.066 90.2% 0.56s Real= 0.14, CPU= 0.14, System= 0.00
17 17.441 92.7% 0.50s Real= 0.17, CPU= 0.14, System= 0.00
18 17.816 95.1% 0.34s Real= 0.17, CPU= 0.12, System= 0.00
19 18.191 97.6% 0.17s Real= 0.18, CPU= 0.19, System= 0.00
20 18.566 100.0% 0.00s Real= 0.15, CPU= 0.14, System= 0.00
Grid Atom Minimum Maximum
Map Type Energy Energy
(kcal/mol) (kcal/mol)
____ ____ _____________ _____________
1 A -0.79 2.01e+05
2 C -0.90 2.01e+05
3 Cl -1.10 2.02e+05
4 NA -1.27 2.00e+05
5 OA -1.40 2.00e+05
6 N -0.97 2.00e+05
7 S -1.11 2.01e+05
8 SA -1.09 2.01e+05
9 HD -0.70 1.05e+05
10 e -5.13 2.88e+00 Electrostatic Potential
11 d 0.00 1.54e+00 Desolvation Potential
* Note: Every pairwise-atomic interaction was clamped at 100000.00
/usr/bin/autogrid4: Successful Completion.
Real= 12.67s, CPU= 12.08s, System= 0.11s