• Step 1:
    Extract EFZ.pdb from 1FK9.pdb
  • Step 2:
    Edit EFZ.pdb with sybyl (modify atom types, bond types and add hydrogen atoms) and save out a mol2 file EFZ_sybyl.mol2 (Take a look at the molecular structure )
  • Step 3:
    Generate gaussian input file EFZ.gcrt if one wants to use RESP charge

    antechamber -fi mol2 -fo gcrt -i EFZ_sybyl.mol2 -o EFZ.gau

  • Step 4a:
    Generate residue topology file EFZ_resp_amber.prepi directly from EFZ.out if one wants to use RESP charge and amber atom types

    antechamber -fi gout -fo prepi -i EFZ.out -o EFZ_resp_amber.prepi -c resp -j both -at amber -rn EFZ

  • Step 4b:
    Generate residue topology file EFZ_resp_amber.prepi directly from EFZ_sybyl.mol2 if one wants to use AM1-bcc charge and amber atom types

    antechamber -fi mol2 -fo prepi -i EFZ_sybyl.mol2 -o EFZ_sybyl_bcc_amber.prepi -j both -c bcc -at amber -rn EFZ

    The atom names in EFZ_resp_amber.prepi may different from those in EFZ.pdb and EFZ_sybyl.mol2. Problems may happen when one load EFZ_resp_amber.prepi and EFZ.pdb to generate topology files (prmtop files) in leap. One may use the following procedure to solve this problem. This time, a cartesian residue topology file is generated.
  • Step 5:
    Generate an ac file from gaussian output file EFZ.out

    antechamber -fi gout -fo ac -i EFZ.out -o -c resp

  • Step 6:
    Extract resp charge to a charge file EFZ.crg from

    antechamber -fi ac -i -c wc -cf EFZ.crg

  • Step 7:
    Read in EFZ.crg and EFZ_sybyl.mol2 and generate an ac file

    Don't forget that EFZ_sybyl.mol2 and EFZ.gau as well as have the same atom sequence order. The charge file QOUT from Step 5 is same to EFZ.crg. One may omit Step 6 and replace EFZ.crg with QOUT in Step 7 to generate

    antechamber -fi mol2 -i EFZ_sybyl.mol2 -c rc -cf EFZ.crg -fo ac -o

  • Step 9:
    Judge the atom type using "atomtype". In this example, gaff atom type is generated

    atomtype -i -o -p gaff

  • Step 10:
    Generate residue topology file EFZ_sybyl_resp_gaff.prepc using "prepgen". In this example a cartesian prep input file is generated with format tag (-f) of "car"

    prepgen -i -o EFZ_sybyl_resp_gaff.prepc -f car

  • Step 11:
    Use parmchk to check the missing force field parameters and generate additional force field parameter file (frcmod) EFZ.frcmod

    parmchk -i EFZ_sybyl_resp_gaff.prepc -o EFZ.frcmod -f prepc

    With EFZ_sybyl_resp_gaff.prepc and EFZ.frcmod, one may use leap to generate topology files for sander etc. The followingleap command generate topology file for the HIV-1 RT inhibitor itself.

    loadamberparams $AMBERHOME/dat/leap/parm/gaff.dat
    loadamberparams EFZ.frcmod
    loadamberprep EFZ_sybyl_resp_gaff.prepc
    saveamberparm EFZ EFZ.prmtop EFZ.prmcrd

  • Step 12:
    One may use two more separated steps to generate input files for resp charge calculation. First, run "espgen" to extract ESP data ( EFZ.esp ) from teh gaussian out file and run "respgen" to generate the retwo-step resp input files ( EFZ.respin1 and EFZ.respin2 ).

    espgen -i EFZ.out -o EFZ.esp

    respgen -i -o EFZ.respin1 -f resp1

    respgen -i -o EFZ.respin2 -f resp2