### KELY: changed the vdw radii for the ones provided by Shuo L. Lin ### extended vdw radii! HUGE diferences in results ### ### Work with this input file, since simplyfies the MS runs and other filetrs ### August 1998 ### # 1st field : residue name; 2nd field: atom name; 3rd field: atom type. # Comments lines must have a '#' character in the 1st column. # # Tentative atom types that will be considered are: # # Mainchain: N CA C O # Code #: 8 1 2 12 # # Group: >CH- >CH2 -CH3 -CH= >C= >C(=O) -C(OO)- S # Code #: 3 4 5 6 6 6 6 7 # # Group: >NH -NH2 >NH+ -NH2+ -NH3+ (C)OO- -OH (C)=O H2O # Code #: 9 9 10 11 11 13 14 14 15 # # Atom types for van der Waals radii using the reduced atom type set: # # Type# Symbol Rvdw Type# Symbol Rdisp Rcoul # 1 CA 1.90 8 N 1.70 1.50 # 2 C 1.75 9 NHn 1.65 1.50 # 3 CH 2.01 10 NH+ 1.65 1.42 # 4 CH2 1.91 11 NHn+ 1.65 1.42 # 5 CH3 1.92 12 O 1.50 1.40 # 6 Csp2 1.82 13 cOO- 1.50 1.38 # 7 S 1.90 14 OH 1.54 1.38 # 15 H2O 1.68 1.38 # # Atom types for scoring: # Full + or H-donor: 1 # Partial + or H-donor: 2 # Partial - or H-acceptor: 3 # H-donor: 4 # H-acceptor: 5 # H-D/A: 6 # Hydrophobic: 7 # C with double bond: 8 # # Atom preference types, see Wallqvist & Covell, Proteins. 25:403-419 (1996) # # The Columns are: # Res Atm vdWT Rdisp Rcoul ScoreT Flex aaTyp # -------------------------------------------- Default XXX XXX 11 1.83 1.83 1 3 12 XXX C?? 4 2.235 2.235 7 1 3 XXX N?? 8 1.83 1.83 4 1 11 XXX O?? 12 1.55 1.55 6 1 16 XXX S?? 7 1.97 1.97 7 2 21 XXX P?? 2 1.87 1.87 7 1 1 XXX FE? 11 1.83 1.83 1 3 12 XXX MG? 11 1.83 1.83 1 3 12 XXX F?? 11 1.83 1.83 1 3 12 XXX BR? 11 1.83 1.83 1 3 12 # -------------------------------------------- ACE ACE C 2 1.87 1.87 7 1 1 ACE O 12 1.55 1.55 5 1 16 ACE CH3 5 2.165 2.165 7 1 3 # -------------------------------------------- ALA ALA N 8 1.83 1.83 4 1 11 ALA CA 1 2.265 2.265 7 1 2 ALA C 2 1.87 1.87 7 1 1 ALA O 12 1.55 1.55 5 1 16 ALA CB 5 2.165 2.165 7 1 3 # -------------------------------------------- ARG ARG N 8 1.83 1.83 4 1 11 ARG CA 1 2.265 2.265 7 1 2 ARG C 2 1.87 1.87 7 1 1 ARG O 12 1.55 1.55 5 1 16 ARG CB 4 2.235 2.235 7 1 3 ARG CG 4 2.235 2.235 7 2 4 ARG CD 4 2.235 2.235 7 2 4 ARG NE 11 1.83 1.83 4 3 15 ARG CZ 2 1.87 1.87 8 3 9 ARG NH1 11 1.83 1.83 2 3 15 ARG NH2 11 1.83 1.83 2 3 15 # -------------------------------------------- ASN ASN N 8 1.83 1.83 4 1 11 ASN CA 1 2.265 2.265 7 1 2 ASN C 2 1.87 1.87 7 1 1 ASN O 12 1.55 1.55 5 1 16 ASN CB 1 2.265 2.265 7 1 3 ASN CG 2 1.87 1.87 8 2 6 ASN ND2 8 1.83 1.83 4 2 18 ASN AD2 8 1.83 1.83 4 2 18 ASN OD1 14 1.55 1.55 5 2 14 ASN AD1 14 1.55 1.55 5 2 14 # -------------------------------------------- ASP ASP N 8 1.83 1.83 4 1 11 ASP CA 1 2.265 2.265 7 1 2 ASP C 2 1.87 1.87 7 1 1 ASP O 12 1.55 1.55 5 1 16 ASP CB 4 2.235 2.235 7 1 3 ASP CG 2 1.87 1.87 8 2 7 ASP OD1 13 1.66 1.66 3 2 19 ASP OD2 13 1.66 1.66 3 2 19 # -------------------------------------------- CYS CYS N 8 1.83 1.83 4 1 11 CYS CA 1 2.265 2.265 7 1 2 CYS C 2 1.87 1.87 7 1 1 CYS O 12 1.55 1.55 5 1 16 CYS CB 4 2.235 2.235 7 1 3 CYS SG 17 1.89 1.89 4 2 21 # -------------------------------------------- GLN GLN N 8 1.83 1.83 4 1 11 GLN CA 1 2.265 2.265 7 1 2 GLN C 2 1.87 1.87 7 1 1 GLN O 12 1.55 1.55 5 1 16 GLN CB 4 2.235 2.235 7 1 3 GLN CG 4 2.235 2.235 7 2 4 GLN CD 2 1.87 1.87 8 2 6 GLN AE2 8 1.83 1.83 4 3 18 GLN NE2 8 1.83 1.83 4 3 18 GLN OE1 14 1.55 1.55 5 3 14 GLN AE1 14 1.55 1.55 5 3 14 # -------------------------------------------- GLU GLU N 8 1.83 1.83 4 1 11 GLU CA 1 2.265 2.265 7 1 2 GLU C 2 1.87 1.87 7 1 1 GLU O 12 1.55 1.55 5 1 16 GLU CB 4 2.235 2.235 7 2 3 GLU CG 4 2.235 2.235 7 2 4 GLU CD 2 1.87 1.87 8 2 7 GLU OE1 13 1.66 1.66 3 3 19 GLU OE2 13 1.66 1.66 3 3 19 # -------------------------------------------- GLY GLY N 8 1.83 1.83 4 1 11 GLY CA 4 2.235 2.235 7 1 2 GLY C 2 1.87 1.87 7 1 1 GLY O 12 1.55 1.55 5 1 16 # -------------------------------------------- HIS HIS N 8 1.83 1.83 4 1 11 HIS CA 1 2.265 2.265 7 1 2 HIS C 2 1.87 1.87 7 1 1 HIS O 12 1.55 1.55 5 1 16 HIS CB 4 2.235 2.235 7 1 3 HIS CG 6 2.04 2.04 7 2 8 HIS ND1 9 1.72 1.72 2 2 13 HIS CD2 15 2.10 2.10 7 2 5 HIS CE1 15 2.10 2.10 8 2 5 HIS NE2 9 1.72 1.72 2 2 13 # -------------------------------------------- ILE ILE N 8 1.83 1.83 4 1 11 ILE CA 1 2.265 2.265 7 1 2 ILE C 2 1.87 1.87 7 1 1 ILE O 12 1.55 1.55 5 1 16 ILE CB 3 2.265 2.265 7 1 3 ILE CG1 4 2.235 2.235 7 1 4 ILE CG2 5 2.165 2.165 7 2 4 ILE CD1 5 2.165 2.165 7 3 4 ILE CD 5 2.165 2.165 7 3 4 # -------------------------------------------- LEU LEU N 8 1.83 1.83 4 1 11 LEU CA 1 2.265 2.265 7 1 2 LEU C 2 1.87 1.87 7 1 1 LEU O 12 1.55 1.55 5 1 16 LEU CB 4 2.235 2.235 7 1 3 LEU CG 3 2.265 2.265 7 2 4 LEU CD1 5 2.165 2.165 7 3 4 2 LEU CD2 5 2.165 2.165 7 3 4 # -------------------------------------------- LYS LYS N 8 1.83 1.83 4 1 11 LYS CA 1 2.265 2.265 7 1 2 LYS C 2 1.87 1.87 7 1 1 LYS O 12 1.55 1.55 5 1 16 LYS CB 4 2.235 2.235 7 1 3 LYS CG 4 2.235 2.235 7 2 4 LYS CD 4 2.235 2.235 7 2 4 LYS CE 4 2.235 2.235 7 3 9 LYS NZ 10 1.65 1.65 1 3 12 # -------------------------------------------- MET MET N 8 1.83 1.83 4 1 11 MET CA 1 2.265 2.265 7 1 2 MET C 2 1.87 1.87 7 1 1 MET O 12 1.55 1.55 5 1 16 MET CB 4 2.235 2.235 7 1 3 MET CG 4 2.235 2.235 7 2 4 MET SD 7 1.97 1.97 7 2 21 MET CE 5 2.165 2.165 7 3 4 # -------------------------------------------- PHE PHE N 8 1.83 1.83 4 1 11 PHE CA 1 2.265 2.265 7 1 2 PHE C 2 1.87 1.87 7 1 1 PHE O 12 1.55 1.55 5 1 16 PHE CB 4 2.235 2.235 7 1 3 PHE CG 6 2.04 2.04 7 2 5 PHE CD1 16 1.99 1.99 7 2 5 PHE CD2 16 1.99 1.99 7 2 5 PHE CE1 16 1.99 1.99 7 2 5 PHE CE2 16 1.99 1.99 7 2 5 PHE CZ 16 1.99 1.99 7 2 5 # -------------------------------------------- PRO PRO N 8 1.83 1.83 4 1 11 PRO CA 1 2.265 2.265 7 1 2 PRO C 2 1.87 1.87 7 1 1 PRO O 12 1.55 1.55 5 1 16 PRO CB 4 2.235 2.235 7 1 3 PRO CG 4 2.235 2.235 7 1 4 PRO CD 4 2.235 2.235 7 1 4 # -------------------------------------------- SER SER N 8 1.83 1.83 4 1 11 SER CA 1 2.265 2.265 7 1 2 SER C 2 1.87 1.87 7 1 1 SER O 12 1.55 1.55 5 1 16 SER CB 4 2.235 2.235 7 1 3 SER OG 14 1.55 1.55 6 2 17 # -------------------------------------------- THR THR N 8 1.83 1.83 4 1 11 THR CA 1 2.265 2.265 7 1 2 THR C 2 1.87 1.87 7 1 1 THR O 12 1.55 1.55 5 1 16 THR CB 3 2.265 2.265 7 1 3 THR OG1 14 1.55 1.55 6 2 17 THR CG2 5 2.165 2.165 7 2 4 # -------------------------------------------- TRP TRP N 8 1.83 1.83 4 1 11 TRP CA 1 2.265 2.265 7 1 2 TRP C 2 1.87 1.87 7 1 1 TRP O 12 1.55 1.55 5 1 16 TRP CB 4 2.235 2.235 7 1 3 TRP CG 6 2.04 2.04 7 2 8 TRP CD1 15 2.10 2.10 7 2 5 TRP CD2 6 2.04 2.04 7 2 8 TRP NE1 9 1.72 1.72 4 2 13 TRP CE2 6 2.04 2.04 7 2 8 TRP CE3 16 1.99 1.99 7 2 5 TRP CZ2 16 1.99 1.99 7 2 5 TRP CZ3 16 1.99 1.99 7 2 5 TRP CH2 16 1.99 1.99 7 2 5 # -------------------------------------------- TYR TYR N 8 1.83 1.83 4 1 11 TYR CA 1 2.265 2.265 7 1 2 TYR C 2 1.87 1.87 7 1 1 TYR O 12 1.55 1.55 5 1 16 TYR CB 4 2.235 2.235 7 1 3 TYR CG 6 2.04 2.04 7 2 10 TYR CD1 16 1.99 1.99 7 2 5 TYR CD2 16 1.99 1.99 7 2 5 TYR CE1 16 1.99 1.99 7 2 5 TYR CE2 16 1.99 1.99 7 2 5 TYR CZ 6 2.04 2.04 7 2 5 TYR OH 14 1.55 1.55 6 2 20 # -------------------------------------------- VAL VAL N 8 1.83 1.83 4 1 11 VAL CA 1 2.265 2.265 7 1 2 VAL C 2 1.87 1.87 7 1 1 VAL O 12 1.55 1.55 5 1 16 VAL CB 3 2.265 2.265 7 1 3 VAL CG1 5 2.165 2.165 7 2 4 VAL CG2 5 2.165 2.165 7 2 4 #-------------------------------------------- OXT XXX OXT 18 1.48 1.48 3 1 19 XXX OT1 18 1.48 1.48 3 1 19 XXX OT2 18 1.48 1.48 3 1 19