I am trying to perform the “Calculate Protein Ionization and Residue pK” protocol on the PDB structure 7EGQ formed by more than 99999 atoms considering the hydrogen atoms.

I understood that this is the cause of the calculation failure giving the error “ERROR: 7EGQ.gbpar.txt does NOT exists” in the file “GBpK_stderr.txt” since the created pdb file (i.e., 7EGQ.gbcoor.pdb) is wrongly written.

I show you the part of this pdb file wrongly written:

ATOM 99997 HE2 TYR 180 232.140 300.929 154.275 1.00 19.90 20

ATOM 99998 CZ TYR 180 231.798 299.178 153.073 1.00 19.90 20

ATOM 99999 OH TYR 180 232.944 299.331 152.327 1.00 19.90 20

ATOM ***** HH TYR 180 232.905 300.176 151.885 1.00 19.90 20

ATOM ***** C TYR 180 225.997 297.592 155.805 1.00 0.00 20

ATOM ***** O TYR 180 225.607 298.594 156.407 1.00 0.00 20

…..

I tried different attempts:

1) I tried to split the PDB file into two models avoiding the limit of number of atoms and I used this file as input structure. Also in this case I had the same error since during the calculation the protocol create the gbcoor.pdb file as unique model.  

2)I tried to modify the alpahgen_memb.inp substituting “open write form unit 1 name GBCOOR_FILE write coor pdb unit 1” in “open write form unit 1 name GBCOOR_FILE write coor card unit 1” and in the same time, I modified the script “ProteinIonizationGBPK_Memb.pm” in the protocol of Pipeline Pilot substituting this commandi line:

# Create alphagen_run.inp file

my \$run_inp = "alphagen_run.inp";

my \$fcoor = "\"".\$molecule_name . ".gbcoor.pdb\"";

my \$fpar = "\"".\$molecule_name . ".gbpar.txt\"";

in

# Create alphagen_run.inp file

my \$run_inp = "alphagen_run.inp";

my \$fcoor = "\"".\$molecule_name . ".gbcoor.crd\"";

my \$fpar = "\"".\$molecule_name . ".gbpar.txt\"";

The protocol created the file 7EGQ.gbcoor.crd but gave the error “ERROR: 7EGQ.gbcoor.pdb does NOT exists” in the file “GBpK_stderr.txt

I would appreciate if somebody could help me providing some suggestions to solve this. Thanks.