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Usage: antechamber options

-i -o -fi and -fo must be appear in command lines and the others are optional

  • -i input file name
  • -fi input file format
  • -o output file name
  • -fo output file format
  • -c charge method
  • -cf charge filename
  • -nc net molecular charge (int)
  • -a additionalt file name
  • -fa additionalt file format
  • -ao additionalt file operation
    • crd : only read in coordinate
    • crg: only read in charge
    • radius: only read in radius (new version)
    • name : only read in atom name
    • type : only read in atom type
    • bond : only read in bond type
  • -m mulitiplicity (2S+1), default is 1
  • -rn residue name, if not available in the input file, default is MOL
  • -rf residue toplogy file name in prep input file, default is molecule.res
  • -mp mopac program name, default is mopac.sh (old version)
  • -mk mopac keyword in a pair of quotation mark (old version)
  • -ek mopac or sqm keyword, inside a pair of quotes (new version)
  • -gk gaussian keyword in a pair of quotation mark
  • -ch check file name for gaussian, default is ‘molecule’ (new version)
  • -gm gaussian memory keyword, inside a pair of quotes, such as”%mem=1000MB” (new version)
  • -gn gaussian number of processors keyword, inside a pair of quotes, such as “%nproc=8” (new version)
  • -gv add keyword to generate gesp file (for Gaussian 09 only) (new version)
    • 1 : yes
    • 0 : no, the default
  • -ge gaussian esp file generated by iop(6/50=1), default is g09.gesp (new version)
  • -df am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac (new version)
  • -at atom type, can be gaff, amber(for PARM94/99/99SB), bcc and sybyl, default is gaff
  • -du fix atom name duplications, can be yes(y) or no(n), default is yes ( default no in old version)
  • -bk 4-character component Id, for ccif (new version)
  • -an adjust atom names: yes(y) or no(n), the default is ‘y’ for ‘mol2’ and ‘ac’ and ‘n’ for the other format (new version)
  • -j atom type and bond type prediction index, default is 4
    • 0 : no assignment
    • 1 : atom type
    • 2 : full bond types
    • 3 : part bond types
    • 4 : atom and full bond type
    • 5 : atom and part bond type
  • -s status information can be 0 (brief), 1 (the default) and 2 (verbose)
  • -eq equalizing atomic charge, default is 1 for ‘-c resp’ and ‘-c bcc’ and 0 for the other charge methods (new version)
    • 0 : no use
    • 1 : by atomic paths
    • 2 : by atomic paths and structural information, i.e. E/Z configurations
  • -pf remove the intermediate files: can be yes (y) and no (n), default is no
  • -pl maximum path length to determin equivalence of atomic charges for resp and bcc, the smaller the value, the faster the algorithm, default is -1 (use full length), set this parameter to 10 to 30 if your molecule is big (# atoms >= 100) (new version)
  • -L list the supported file formats and charge methods

List of the File Formats

file format type abbre. index file format type abbre. index
Antechamber ac 1 Sybyl Mol2 mol2 2
PDB pdb 3 Modifiled PDB mpdb 4
AMBER PREP (int) prepi 5 AMBER PREP (car) prepc 6
Gaussian Z-Matrix gzmat 7 Gaussian Cartesia gcrt 8
Mopac Internal mopint 9 Mopac Cartesian mopcrt 10
Gaussian Output gout 11 Mopac Output mopout 12
Alchemy alc 13 CSD csd 14
MDL mdl 15 Hyper hin 16
AMBER Restart rst 17 Jaguar Cartesian jcrt 18
Jaguar Z-Matrix jzmat 19 Jaguar Output jout 20
Divcon Input divcrt 21 Divcon Output divout 22
SQM Input sqmcrt 23 SQM Output sqmout 24
Charmm charmm 25 Gaussian ESP gesp 26
Component cif ccif 27      

AMBER restart file can only be read in as additional file. Old version may just support type 1-17.

List of the Charge Methods

charge method abbre. index charge method abbre. index
RESP resp 1 AM1-BCC bcc 2
CM1 cm1 3 CM2 cm2 4
ESP (Kollman) esp 5 Mulliken mul 6
Gasteiger gas 7 Read in charge rc 8
Write out charge wc 9 Delete Charge dc 10

Old version may just not support type 3 and 10.

  • 在老版Amber中是使用Mopac算电荷的, 后来的版本就加入了sqm程序来算电荷. 在老版本中支持cm1,cm2等电荷, 但新版本中SQM和高斯都不能算CM1和CM2.
  • 高斯结果只能转出成resp(用gesp)和esp(用gout), 不能转成Mulliken,虽然out里面有Mulliken Charge, 但和BCC算出的Mulliken相差甚远..另外gesp不能产生ESP电荷.
  • 用antechamber算Gasteiger, Mulliken和AM1-BCC都是可以的, 后两者需要调用sqm. 即使用gout也不能产生出BCC和Mulliken.
  • 转为pdb是没有电荷的.mol2/ac/mpdb/都可以带电荷.



# Calculate bcc charge for input mol2
antechamber -i ligand.mol2 -fi mol2 -o ligand_bcc.mol2 -fo mol2 -c bcc -pf y
# Convert file to prepi and use parmchk to generate amber input parameter
antechamber -i ligand_bcc.mol2 -fi mol2 -o ligand_bcc.prep -fo prepi -pf y
parmchk -i ligand.prep -f prepi -o ligand.frcmod
# in tleap: loadAmberPrep ligand.frcmod

# Directly generate prepi file from mol2 with bcc charge, not commend
antechamber -i ligand.mol2 -fi mol2 -o small_bcc.prep -fo prepi -c bcc -pf y

# Convert mol2 <-> Gaussian input/output for charge calculation for esp/resp
antechamber -i ligand.mol2 -fi mol2 -o ligand.gjf -fo gcrt -pf y -gn "%nproc=8" -gm "%mem=1000MB"
antechamber -i ligand.log -fi gout -o ligand_resp.mol2 -fo mol2 -c resp -pf y

# Write out the charge to charge file
antechamber -i ligand_bcc.mol2 -fi mol2 -c wc -cf ligand_c.crg
# Load known charge to molecule. The charge file ligand_c.crg is f10.8  8charge/per line
antechamber -i ligand.mol2 -fi mol2 -o ligand_c.mol2 -fo mol2 -c rc -cf ligand_c.crg


  • 在使用antechamber转格式时, mol2输出时默认gaff 原子类型, 要保持原有类型, 使用-at sybyl或者-j 0/2/3
  • 转mol2键级时, 羧基antechamber会解释为1/2键级, 而一般mol2是ar.



  • -i input file name
  • -o output file name(ac)
  • -f input file format(ac (the default) or mol2)
  • -p amber or gaff or bcc or gas or sybyl, it is supressed by “-d” option
  • -d atom type defination file, optional
  • -a do post atom type adjustment (it is or sybyl applied with “-d” option) 1: yes, 0: no (the default)

类型定义文件在$AMBERHOME/dat/antechamber, ATOMTYPE_AMBER.DEF (amber), ATOMTYPE_GFF.DEF (general amber force field), ATOMTYPE_BCC.DEF (AM1-BCC), ATOMTYPE_SYBYL.DEF (sybyl) and ATOMTYPE_GAS.DEF (gasteiger). 使用-p来选择.


ATOM      1  C   <1>     1       1.208   0.697   0.000  0.000000      C.ar
ATOM      2  C   <1>     1       2.494   1.441   0.000  0.000000       C.3
ATOM      3  H1  <1>     1       2.295   2.512  -0.000  0.000000         H
ATOM      4  O   <1>     1       3.238   1.099  -1.158  0.000000       O.3


  • -i input file name
  • -o output file name
  • -f file format (ac or mol2)
  • -j judge bond type level option, default is part
    1. full full judgement
    2. part partial judgement, only do reassignment according to known bond type information in the input file
  • -s stop running if APS (atomic penality score) is not available
    1. 0 - no, all the related bonds are frozen, the default
    2. 1 - yes

输出的bond types (single (1), double (2), triple (3), aromatic single (7), aromatic double (8), aromatic(10), delocalized (9) and conjugated (6))

参数文件在 APS.DAT in $AMBERHOME/dat/antechamber

输出文件中,储存在BOND部分.四个数字: 键序号, 两个原子序号, 键类型, 原子名(原子部分对应,非类型).

BOND    1    1    2    1      C    C
BOND    2    1    7    8      C    C
BOND    3    1   16    7      C    C
BOND    4    2    3    1      C   H1


  • -i input file name in ac format
  • -o output file name
  • -f output file format(pdb or ac, optional, default is ac)
  • -p bcc parm file name (optional))
  • -s status information, can be 0 (brief), 1 (the default) and 2 (verbose)
  • -j atom and bond type judge option, default is 0)
    1. 0: No judgement
    2. 1: Atom type
    3. 2: Full bond type
    4. 3: Partial bond type
    5. 4: Atom and full bond type
    6. 5: Atom and partial bond type


  1. antechamber

◆ 本文地址: http://platinhom.github.io/2015/09/16/antechamber/, 转载请注明 ◆

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Source 类别: CompCB  标签: CompBiol  MD