*****  Making TINKER-AMBER input file with Facio 11.8.6 *****

Force field parameters are amber99.prm, charmm27.prm and oplsaal.prm.

Procedure to make TINKER-AMBER input file :

(1) If there are missing hygrogens, add them using 
    "Add Hydrogen Atoms to Protein PDB by ATOM Record" in FMO menu.


(2) Delete HETATM records (if any) with text editor.
    The resulted file is PDB1 file.

(3) Load PDB1 to Facio and and check missing bonds. 
    If there are missing bonds, make bonds.
    Save as HETATM/CONECT record PDB file.
    The resulted file is PDB2 file.

    In this step, TER record which exists as dummy atom 
    in PDB1 is also deleted.

    At this point, you have two PDB files 
    for an identical protein.

    PDB1 : in ATOM record
    PDB2 : in HETATM/CONECT record

(4) Open FMO Menu >> TINKER-AMBER Input File Maker

(5) Specify PDB1 and PDB2.

(6) Select force field parameter.

(7) Click "Make TINKER-AMBER Input" button, and
    input file, Amber.xyz is generated. And at the same time,
    the corresponding batch file and key file for TINKER-AMBER calculation
    are also generated.

*************************************************************

Samples included in Tinker-Amber folder.

　*_Hadd.pdb         　ATOM record PDB            (This is PDB1.)
　*_Hadd_HETATM.pdb  　HETATM/CONECT record PDB   (This is PDB2.)
　*_Amber.xyz        　TINKER-AMBER input file generated by Facio


(in the Other_Samples)

2ol9_Hadd.pdb　　2ol9_Hadd_HETATM.pdb　　2ol9_Amber.xyz
2cga_Hadd.pdb　　2cga_Hadd_HETATM.pdb　　2cga_Amber.xyz
1yjp_Hadd.pdb　　1yjp_Hadd_HETATM.pdb　　1yjp_Amber.xyz
1crn_Hadd.pdb　　1crn_Hadd_HETATM.pdb　　1crn_Amber.xyz
1b9g_Hadd.pdb　　1b9g_Hadd_HETATM.pdb　　1b9g_Amber.xyz


If you use Tinker's optimize.exe, calculations of 2cga, 1crn and 1b9g
will be stopped with the following error message.

'Optimize -- Too many Parameters, Increase the Value of MAXOPT'

To avoid this error, increase the value of MAXOPT
which is defined in sizes.i of Tinker source files
and recompile TINKER.

Or use Tinker's minimize.exe and newton.exe.


********************************************************

(in the folder 1uao)

1uao_model_1.pdb
1uao_model_1_C.pdb
1uao_model_1_C_HETATM.pdb

1uao_Amber.xyz
1uao_Amber-1.xyz
1uao_Amber.bat
1uao_Amber.key

1uao_Charmm.xyz
1uao_Charmm-1.xyz
1uao_Charmm.bat
1uao_Charmm.key

1uao_Oplsaal.xyz
1uao_Oplsaal-1.xyz
1uao_Oplsaal.bat
1uao_Oplsaal.key


There is no missing hydrogen in 1uao.pdb,
but there are wrong descriptions in Atom Name Field 
(from column 13 to column 16) of Atom record.
They are wrong, however, they are frequently used 
especially in structures obtained by NMR experiments.

Please refer to the following web site for the Atom record format.

http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html


1uao_model_1.pdb is MODEL 1 extracted from 1uao.pdb

1uao_model_1.pdb
...
ATOM      5  HA2 GLY A   1      -7.677  -1.140   2.309  1.00  0.00           H  
ATOM      6  HA3 GLY A   1      -7.085   0.336   3.073  1.00  0.00           H  
ATOM      7  H1  GLY A   1      -5.778  -1.527   4.462  1.00  0.00           H  
ATOM      8  H2  GLY A   1      -7.214  -2.365   4.112  1.00  0.00           H  
ATOM      9  H3  GLY A   1      -7.273  -0.879   4.933  1.00  0.00           H  
...
ATOM     83 HG21 THR A   6       5.309   0.265   3.208  1.00  0.00           H  
ATOM     84 HG22 THR A   6       4.906  -1.371   3.728  1.00  0.00           H  
ATOM     85 HG23 THR A   6       3.625  -0.188   3.464  1.00  0.00           H  


############################################################
   Facio can repair wrong atom name field.
   Use FMO Menu >> PDB Atom Name Field Converter
############################################################


1uao_model_1_repaired.pdb
...
ATOM      5 1HA  GLY A   1      -7.677  -1.140   2.309  1.00  0.00           H  
ATOM      6 2HA  GLY A   1      -7.085   0.336   3.073  1.00  0.00           H  
ATOM      7 1H   GLY A   1      -5.778  -1.527   4.462  1.00  0.00           H  
ATOM      8 2H   GLY A   1      -7.214  -2.365   4.112  1.00  0.00           H  
ATOM      9 3H   GLY A   1      -7.273  -0.879   4.933  1.00  0.00           H  
...
ATOM     83 1HG2 THR A   6       5.309   0.265   3.208  1.00  0.00           H  
ATOM     84 2HG2 THR A   6       4.906  -1.371   3.728  1.00  0.00           H  
ATOM     85 3HG2 THR A   6       3.625  -0.188   3.464  1.00  0.00           H  

******************************************************************************



