! all lines beginning with an exclamation mark are comments ! be sure to change the file names for the pdb file, charges file, ! and output grid file before using this script ! UHBD input file test.inp !this reads in the pdb file, in the converted amber-like format read coord mol1 file "ex.amb" fpdb ascii end !this reads in the charges set charge file "qtable.dat" amber end print rpar mol1 end print apar mol1 end ! main chain atoms edit mol1 radius atnam N 1.54 end edit mol1 radius atnam HN 1.20 end edit mol1 radius atnam H 1.20 end edit mol1 radius atnam CA 2.00 end edit mol1 radius atnam C 1.74 end edit mol1 radius atnam O 1.40 end ! N-terminal amino group edit mol1 radius atnam HN1 1.20 end edit mol1 radius atnam HN2 1.20 end edit mol1 radius atnam HN3 1.20 end ! standard aliphatic side chain edit mol1 radius atnam CB 2.00 end edit mol1 radius atnam CG 2.00 end edit mol1 radius atnam CD 2.00 end edit mol1 radius atnam CE 2.00 end ! C-terminal residue edit mol1 radius resid LYSC atnam NZ 1.54 end edit mol1 radius resid LYSC atnam HZ1 1.20 end edit mol1 radius resid LYSC atnam HZ2 1.20 end edit mol1 radius resid LYSC atnam HZ3 1.20 end edit mol1 radius resid LYSC atnam OT1 1.40 end edit mol1 radius resid LYSC atnam OT2 1.40 end edit mol1 radius resid LYSC atnam O 1.40 end edit mol1 radius resid LYSC atnam OT 1.40 end edit mol1 radius resid LYSC atnam OXT 1.40 end ! residue side chains: C D E F H I K L M N Q R S T V W Y ! (A G P are handled by standard radii definitions) edit mol1 radius resid ARG atnam NE 1.54 end edit mol1 radius resid ARG atnam HE 1.20 end edit mol1 radius resid ARG atnam CZ 1.74 end edit mol1 radius resid ARG atnam NH1 1.54 end edit mol1 radius resid ARG atnam HH11 1.20 end edit mol1 radius resid ARG atnam HH12 1.20 end edit mol1 radius resid ARG atnam NH2 1.54 end edit mol1 radius resid ARG atnam HH21 1.20 end edit mol1 radius resid ARG atnam HH22 1.20 end edit mol1 radius resid ASN atnam CG 1.74 end edit mol1 radius resid ASN atnam OD1 1.40 end edit mol1 radius resid ASN atnam ND2 1.54 end edit mol1 radius resid ASN atnam HD21 1.20 end edit mol1 radius resid ASN atnam HD22 1.20 end edit mol1 radius resid ASP atnam CG 1.74 end edit mol1 radius resid ASP atnam OD1 1.40 end edit mol1 radius resid ASP atnam OD2 1.40 end edit mol1 radius resid CYS atnam SG 1.80 end edit mol1 radius resid CYS atnam HG 1.20 end edit mol1 radius resid CYX atnam SG 1.80 end edit mol1 radius resid GLN atnam CD 1.74 end edit mol1 radius resid GLN atnam OE1 1.40 end edit mol1 radius resid GLN atnam NE2 1.54 end edit mol1 radius resid GLN atnam HE21 1.20 end edit mol1 radius resid GLN atnam HE22 1.20 end edit mol1 radius resid GLU atnam CD 1.74 end edit mol1 radius resid GLU atnam OE1 1.40 end edit mol1 radius resid GLU atnam OE2 1.40 end edit mol1 radius resid HIS atnam CG 1.74 end edit mol1 radius resid HIS atnam CD2 1.86 end edit mol1 radius resid HIS atnam ND1 1.54 end edit mol1 radius resid HIS atnam CE1 1.86 end edit mol1 radius resid HIS atnam NE2 1.54 end edit mol1 radius resid HIS atnam HE2 1.20 end edit mol1 radius resid HID atnam CG 1.74 end edit mol1 radius resid HID atnam CD2 1.86 end edit mol1 radius resid HID atnam ND1 1.54 end edit mol1 radius resid HID atnam HD1 1.20 end edit mol1 radius resid HID atnam CE1 1.86 end edit mol1 radius resid HID atnam NE2 1.54 end edit mol1 radius resid HIP atnam CG 1.74 end edit mol1 radius resid HIP atnam CD2 1.86 end edit mol1 radius resid HIP atnam ND1 1.54 end edit mol1 radius resid HIP atnam HD1 1.20 end edit mol1 radius resid HIP atnam CE1 1.86 end edit mol1 radius resid HIP atnam NE2 1.54 end edit mol1 radius resid HIP atnam HE2 1.20 end edit mol1 radius resid HISL atnam CG 1.74 end edit mol1 radius resid HISL atnam CD2 1.86 end edit mol1 radius resid HISL atnam ND1 1.54 end edit mol1 radius resid HISL atnam CE1 1.86 end edit mol1 radius resid HISL atnam NE2 1.54 end edit mol1 radius resid HISL atnam CU 1.40 end edit mol1 radius resid HISL atnam ZN 1.40 end edit mol1 radius resid HISR atnam CG 1.74 end edit mol1 radius resid HISR atnam CD2 1.86 end edit mol1 radius resid HISR atnam ND1 1.54 end edit mol1 radius resid HISR atnam CE1 1.86 end edit mol1 radius resid HISR atnam NE2 1.54 end edit mol1 radius resid HISR atnam HE2 1.20 end edit mol1 radius resid HISR atnam CU 1.40 end edit mol1 radius resid HISR atnam ZN 1.40 end edit mol1 radius resid ILE atnam CG1 2.00 end edit mol1 radius resid ILE atnam CG2 2.00 end edit mol1 radius resid ILE atnam CD1 2.00 end edit mol1 radius resid ILE atnam CD 2.00 end edit mol1 radius resid LEU atnam CD1 2.00 end edit mol1 radius resid LEU atnam CD2 2.00 end edit mol1 radius resid LYS atnam NZ 1.54 end edit mol1 radius resid LYS atnam HZ1 1.20 end edit mol1 radius resid LYS atnam HZ2 1.20 end edit mol1 radius resid LYS atnam HZ3 1.20 end edit mol1 radius resid MET atnam SD 1.80 end edit mol1 radius resid METN atnam SD 1.80 end edit mol1 radius resid PHE atnam CG 1.74 end edit mol1 radius resid PHE atnam CD1 1.86 end edit mol1 radius resid PHE atnam CD2 1.86 end edit mol1 radius resid PHE atnam CE1 1.86 end edit mol1 radius resid PHE atnam CE2 1.86 end edit mol1 radius resid PHE atnam CZ 1.86 end edit mol1 radius resid SER atnam OG 1.40 end edit mol1 radius resid SER atnam HG 1.20 end edit mol1 radius resid THR atnam OG1 1.40 end edit mol1 radius resid THR atnam HG1 1.20 end edit mol1 radius resid THR atnam CG2 2.00 end edit mol1 radius resid TRP atnam CG 1.74 end edit mol1 radius resid TRP atnam CD1 1.86 end edit mol1 radius resid TRP atnam NE1 1.54 end edit mol1 radius resid TRP atnam HE1 1.20 end edit mol1 radius resid TRP atnam CD2 1.74 end edit mol1 radius resid TRP atnam CE2 1.74 end edit mol1 radius resid TRP atnam CZ2 1.86 end edit mol1 radius resid TRP atnam CH2 1.86 end edit mol1 radius resid TRP atnam CE3 1.86 end edit mol1 radius resid TRP atnam CZ3 1.86 end edit mol1 radius resid TYR atnam CG 1.74 end edit mol1 radius resid TYR atnam CD1 1.86 end edit mol1 radius resid TYR atnam CD2 1.86 end edit mol1 radius resid TYR atnam CE1 1.86 end edit mol1 radius resid TYR atnam CE2 1.86 end edit mol1 radius resid TYR atnam CZ 1.74 end edit mol1 radius resid TYR atnam OH 1.40 end edit mol1 radius resid TYR atnam HH 1.20 end edit mol1 radius resid VAL atnam CG1 2.00 end edit mol1 radius resid VAL atnam CG2 2.00 end print mpar mol1 srad 1.4 end print geom mol1 srad 1.4 end elec calc mol1 dime 128 128 128 center grid 1.0 ions 075. bcfl 1 dhrad 30.0 maxi 400 conv 1e-8 smooth ! dradfact 1.0 ! eradadd 1.5 end !this writes the electrostatic grid file write phi file "ex.grd" ascii end quit