Need run a set of programs (atomtype, bondtype, am1bcc, prepgen etc) to Generate an amino-acid-like residue topology file (prep input file), you may However, in some special cases, for instance, to Separated programs to do molecular format conversion, atom type assignmentĪnd charge generation etc. In most of cases, one should use this program instead of a series of The antechamber program itself is the main program of Antechamber package. The above script finds all the files with extension of "mol2" in the current directory.įor each file, antechamber is run to get Mulliken charges. j atom and bond type judge option, default is 0)Īntechamber -i $mol_dir.mol2 -fi mol2 -fo ac -o $mol_dir.ac -c mulĪm1bcc -i $mol_dir.ac -f ac -o $mol_dir.ac -j 5
f output_file_format(pdb or ac, optional, default is ac) Usage: am1bcc -i input_file_name in ac format you can generate AM1-Mulliken charge using Revise them and run am1bcc with "-j" set to 0, which means no assignment to be performed.īear in mind that am1bcc dose not run mopac to get AM1-Mulliken charges itself, which is If there is some problem with the assignments, you may manually This program first callsĪtomtype and bondtype to do atom type and bond type perception and then doesīond Charge Correction (BCCPARM.DAT in $AMBERHOME/dat/antechamber). Page, where there are some tips on how to use antechamber programs efficiently and properly.Īm1bcc reads in an ac file to assign atom types and bond types according to AM1-BCCĭefinitions (ATOMTYPE_BCC.DEF in $AMBERHOME/dat/antechamber). More examples and tutorialsĪre available in other pages. Prep and frcmod files to be read by LEaP. At the bottom of this page, we provideĪn example ( TP) to demonstrate how to use antechamber programs to generate Journal of Chemical Information and Computer Science. As to algorithmsīeyond those programs, please refer to our paper submitted to Package (circa 2007 for more recent information see theĪmberTools Manual for the latest informationĮxecute the program with the -h option). In the following, we list the usage of the programs in the antechamber
May be useful outside the Amber family of programs as well. The algorithms behind these manipulations As anĪccessory module in the AmberTools package, antechamber can generate inputĪutomatically for most organic molecules in a database. (4) finding missing force field parameters and supplying reasonable and similar substitutes. (2) recognizing bond type (2) judging the atomic equivalence (3) generating residue topology file Is devoted to solve the following problems during the MM calculations: (1) recognizing the atom type Antechamber is a set of auxiliary programs for molecular mechanic (MM) studies.
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