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

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

List of the Charge Methods

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.

例子:

用ligand.mol2作例子:

# 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

Update

• 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.

子程序

atomtype

• -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.

原子类型输出在最后一列.

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

bondtype

• -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

am1bcc

• -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

Reference

1. antechamber