Amber 10 Tutorial. antechamber: strange molecules get parameter files. antechamber & leap. antechamber is predominantly a file converter. However, it can be used in conjunction with leap to build parameter files that can be used to run MD and other simulations. sustiva.pdb.
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antechamber: strange molecules get parameter files
What makes the antechamber/leap combination so powerful is the original format of the information that is fed into it.
Notice that on the left there is no detailed information given. Only atom #, atom type, and position. With this antechamber and leap can generate parameter files.
The SUS label on the atoms here is important because it will be the label leap will use later for the sustiva unit.
4 AchamberSUS.sh* 8 ATOMTYPE.INF 4 sus.leap
4 ANTECHAMBER_AC.AC 4 delete.com* 92 sustiva.crd
4 ANTECHAMBER_AC.AC0 4 divcon.pdb 4 sustiva.frcmod
4 ANTECHAMBER_AM1BCC.AC 16 leap.log 4 sustiva.pdb
4 ANTECHAMBER_AM1BCC_PRE.AC 4 mopac.in 4 sustiva.prepin
4 ANTECHAMBER_BOND_TYPE.AC 40 mopac.out 376 sustiva.top
4 ANTECHAMBER_BOND_TYPE.AC0 4 mopac.pdb 164 sustivawh2o.lpdb
4 ANTECHAMBER_PREP.AC 4 NEWPDB.PDB
4 ANTECHAMBER_PREP.AC0 4 PREP.INF