*****  TINKER-AMBER̓̓t@C쐬@\  iFacio 11.8.6j*****

͏p[^́Aamber99.prm, charmm27.prm, oplsaal.prmg܂B

̗́Aȉ̒ʂłB
iPjFMOj[Add Hydrogen Atoms to Protein PDB by ATOM RecordŐf⊮B

@@@fq̌@PDBt@CɂẮÃXebv̍Ƃ́AKvB


iQjqȂHETATM̂́AeLXgGfB^
@@@폜B
@@@ꂽt@CPDB1ƂB

iRjFacioPDB1ǂݍ݁AĂ錋Ȃǂ΁A
@@@⊮AHETATM/CONECT`PDBt@CƂĕۑB
@@@̃t@CPDB2ƂB

@@@̑ŁA_~[qƂđ݂ĂTERR[hB

iSjFMOj[TINKER-AMBER Input File MakerJ

iTjPDB1PDB2w肷B

iUj͏p[^IB

iVjMake TINKER-AMBER Input {^NbN
@@@Amber.xyzƂt@CŁA̓t@C쐬B
@@@ɁANp̃ob`t@Ckeyt@CB

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

Tinker-AmberɓTv

@@*_Hadd.pdb         @ATOM`PDBt@C@iPDB1j
@@*_Hadd_HETATM.pdb  @HETATM/CONECT`PDBt@C@iPDB2j
@@*_Amber.xyz        @TINKER-AMBER̓t@C@
@@@@@@@@@@@@iFacioTINKER-AMBER̓t@Cj

(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


AATinkeroptimize.exeg
2cga, 1crn, 1b9ǧvZۂɍsȂƂ
ȉ̂悤ȃbZ[WłČvZ~܂Ă܂܂B

uOptimize -- Too many Parameters, Increase the Value of MAXOPT v

邽߂ɂ́ATINKER̃\[Xt@Csizes.i 
`ĂMAXOPTƂp[^̒l傫
TINKERăRpCKv܂B

邢́Aminimize.exenewton.exegĉB

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

(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


1uao.pdbɂ́Aɐfq܂A
PDBt@CAtom Name tB[hi13J16J܂ł̃f[^j
肪܂BNMRɂċ߂ꂽ\ɓɑ󂯂܂B
iԈLqAĂ܂Bj

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


1uao_model_1.pdb́A1uao.pdbMODEL 1𔲂o

1uao_model_1.pdb iAtom Name Fieldɖ肠j
...
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  


FacioFMO Menu  PDB Atom Name Field ConvertergƁA
̊ԈႢC邱Ƃł܂B


1uao_model_1_C.pdb iAtom Name FieldĆj
...
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  

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


