GPF file prepared by Meeko

[vsheg]

Hi, I'm using Meeko's mk_prepare_receptor.py (v0.5.0 from PyPI) and I've noticed that in a generated GPF file some atom types (Cl and CL and Br and BR) are duplicated.

receptor.gpf

parameter_file boron-silicon-atom_par.dat
npts 106 106 106
gridfld receptor.maps.fld
spacing 0.375
receptor_types A NA C N HD P OA SA
ligand_types HD C A N NA OA F P SA S Cl CL Br BR I Si B
receptor receptor.pdbqt
gridcenter 45.423 41.112 40.872
smooth 0.500
map receptor.HD.map
map receptor.C.map
map receptor.A.map
map receptor.N.map
map receptor.NA.map
map receptor.OA.map
map receptor.F.map
map receptor.P.map
map receptor.SA.map
map receptor.S.map
map receptor.Cl.map
map receptor.CL.map
map receptor.Br.map
map receptor.BR.map
map receptor.I.map
map receptor.Si.map
map receptor.B.map
elecmap receptor.e.map
dsolvmap receptor.d.map
dielectric -42.000

As I can see from AutoDock 4.2 User Guide, parameters for Br and BR, Cl and CL are the same.

❓: Why Meeko generates output with duplicated atom types?

---

Also, I have strange behaviour with AutoGrid4. When I run it with GPF generated by Meeko, I see a strange error

autogrid4 -p receptor.gpf receptor.pdbqt 

Output with the error

...
Output Grid Map 12:   receptor.CL.map
GPF> map receptor.Br.map
Output Grid Map 13:   receptor.Br.map
GPF> map receptor.BR.map
Output Grid Map 14:   receptor.BR.map
GPF> map receptor.I.map
autogrid4: ERROR:  Too many "map" keywords (15);  the "ligand_types" command declares only 14 atom types.
Remove a "map" keyword from the GPF.
autogrid4: ERROR:  Too many "map" keywords (15);  the "ligand_types" command declares only 14 atom types.
Remove a "map" keyword from the GPF.
autogrid4: Unsuccessful Completion.

I figured out, that when I decrease the number of atom specific types and maps to ≤14, AutoGrid4 works fine. I tried with AutoGrid from AutoDock Suite (Win) and from Bioconda (macOS).

When I use the patched version provided by WaterKit (Linux), everything works fine with any number or atom types.

❓: Is it expected behaviour of AutoGrid4 to not accept GPF with 15+ ligand atom types?

---

I would really appreciate it if you help me to understand this. Thank you

[rwxayheee]

Hi @vsheg

Is it expected behaviour of AutoGrid4 to not accept GPF with 15+ ligand atom types?

This might have something to do with a hard limit of 16 for the total number of maps (1 desolvation + 1 electrostatic + at most 14 ligand affinity maps). In autogrid4, the number 16 is set in src/autodock/autocomm.h:

#define MAX_MAPS_PAD 0       // Use this to pad MAX_MAPS to a power of 2, for presumably-faster memory access
#define NUM_NON_VDW_MAPS 2   // Number of electrostatic and desolvation maps
#define MAX_ATOM_TYPES (16 - NUM_NON_VDW_MAPS)    /* Maximum number of atom types set to keep MAX_MAPS a power of 2 */
#define MAX_MAPS (MAX_ATOM_TYPES + NUM_NON_VDW_MAPS + MAX_MAPS_PAD) /* Maximum number of energy maps        */
                            /* 0,1,2,... are for atomic interactions          */
                            /* last two are for electrostatics and desolvation */

#define VECLENMAX    16     /* For AVS fld files...     

This number is increased to 50 in the patched version with WaterKit

[vsheg]

@rwxayheee
Thank you for the detailed explanation, now I understand how limits work