HIV-1 RT /EFZ

• 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 EFZ_resp.ac from gaussian output file EFZ.out
  
  antechamber -fi gout -fo ac -i EFZ.out -o EFZ_resp.ac -c resp
  
  
• Step 6:
  Extract resp charge to a charge file EFZ.crg from EFZ_resp.ac
  
  antechamber -fi ac -i EFZ_resp.ac -c wc -cf EFZ.crg
  
  
• Step 7:
  Read in EFZ.crg and EFZ_sybyl.mol2 and generate an ac file EFZ_sybyl_resp.ac
  
  Don't forget that EFZ_sybyl.mol2 and EFZ.gau as well as EFZ_resp.ac 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 EFZ_sybyl_resp.ac
  
  antechamber -fi mol2 -i EFZ_sybyl.mol2 -c rc -cf EFZ.crg -fo ac -o EFZ_sybyl_resp.ac
  
  
• Step 9:
  Judge the atom type using "atomtype". In this example, gaff atom type is generated EFZ_sybyl_resp_gaff.ac
  
  atomtype -i EFZ_sybyl_resp.ac -o EFZ_sybyl_resp_gaff.ac -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 EFZ_sybyl_resp_gaff.ac -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 EFZ_resp.ac -o EFZ.respin1 -f resp1
  respgen -i EFZ_resp.ac -o EFZ.respin2 -f resp2