4-Hydroxyl-Proline (PR4)

• Step 1:
  Prepare two mol2 files: alpha and beta conformatons for ACE-PR4-ACE (Take a look at the molecular structure )
  
• Step 2:
  Generate two gaussian input files: alpha and beta using the following antechamber command:
  
  antechamber -fi mol2 -fo gzmat -i pro4a.mol2 -o pro4a.gau
  antechamber -fi mol2 -fo gzmat -i pro4b.mol2 -o pro4b.gau
  
  Do the following modifications on pro4a.gau and pro4b.gau:
  change opt to popt in the keyword section
  freeze t19 and t21 during the minimization with a tag of "F"
  
• Step 3:
  Run gaussian to get two output files: alpha and beta
  
• Step 4:
  Extract ESP files from gaussian output files ( alpha and beta ) and merge them together pro4.esp ; then prepare input files for two-stage resp fitting ( Step I and Stage II ); finally run resp program to get resp charge ( Pro4.crg ).
  
  espgen -i pro4a.out -o pro4a.esp
  espgen -i pro4b.out -o pro4b.esp
  cat pro4a.esp pro4b.esp >pro4.esp
  respgen -i pro4a.mol2 -o pro4-step1.respin -f resp1 respgen -i pro4a.mol2 -o pro4-step2.respin -f resp2
  
  Manually revision pro4-step1.respin and pro4-step2.respin are necessary in this example since respgen cannot generate input files for multiple molecules.
  
  
• Step 5:
  Load pro4.crg and generate an ac file ( pro4.ac ).
  antechamber -fi mol2 -fo ac -i pro4a.mol2 -o pro4.ac -c rc -cf pro4.crg
  
  However, if one only use one conformation, he may generate an ac file from the gaussian output file with charge method tag set to "resp" directly.
  
• Step 6:
  Read in pro4.ac and a mainchain defination file mainchain.pro4 to generate prep input file 4-OH-PROfor 4-OH-PRO.
  
  In mainchain defination file, HEAD_NAME is the atom connected to the immediately previous residue and TAIL_NAME is the atom connected to the immediately behide reside; OMIT_NAME(s) is (are) not a part of the residue, however they are necessary to maintain a proper chemical environment; MAINCHAIN are mainchain atoms (HEAD_NAME and TAIL_NAME are mainchain atoms automatically); PRE_HEAD_TYPE and POST_TAIL_TYPE N are the atom types of atoms in other residues that are connected to the head and tail, respectively. CHARGE is the net charge of the residue in question.
  
  prepgen -i pro4.ac -o pro4.prepi -f prepi -m mainchain.pro4 -rn PR4 -rf pro4.res
  
  For PR4 , HEAD_NAME is N1; TAIL_NAME is C7 and all the atoms in green and yellow are omitted atoms. The PRO_HEAD_TYPE and POST_TAIL_TYPE are C and N respectively
  
• Step 7:
  With pro4.prepi, one may use leap to generate topolgy files for sander etc. Here we generate a topology file for ALA-PRO4-ALA with leap.
  
  loadamberprep pro4.prep
  aa =sequence {ALA PR4 ALA}
  saveamberparm aa ala-pr4-ala.prmtop ala-pr4-ala.prmcrd