inhibitor complex par/top files

Jodi Lubetsky jodi at PHARM.MED.YALE.EDU
Thu Nov 5 18:12:25 EST 1998


xplor users:

I am working on an enzyme-inhibitor complex and am having problems
maintaining the aromatic geometry of the inhibitor during positional
refinement. I created the inhibitor with InsightII and then used XPLOR2D to
make the parameter files. I cannot find anything wrong with my topology and
parameter files that might result in this problem, but I am attaching it below
anyway. I would appreciate any suggestion anyone might have.

Jodi

********************************************************************************
Remarks hpp.top
Remarks Created by XPLO2D V. 960804/2.1 at Wed Nov 4 10:28:50 1998 for user
jodi
Remarks Auto-generated by XPLO2D from file enol_o.pdb
Remarks You *MUST* check/edit MASSes and CHARges !!!
Remarks Check DONOrs and ACCEptors
Remarks Verify IMPRopers yourself
Remarks DIHEdrals which are not flat are commented out

 set echo=false end

 { edit masses if necessary }
 MASS OX1    15.99940 ! 15.99940 + 1.008 for each H
 MASS CX2    13.01900 ! 12.01100 + 1.008 for each H
 MASS CX3    12.01100 ! 12.01100 + 1.008 for each H
 MASS CX4    13.01900 ! 12.01100 + 1.008 for each H
 MASS CX5    12.01100 ! 12.01100 + 1.008 for each H
 MASS CX6    12.01100 ! 12.01100 + 1.008 for each H
 MASS CX7    12.01100 ! 12.01100 + 1.008 for each H
 MASS OX8    15.99940 ! 15.99940 + 1.008 for each H
 MASS OX9    15.99940 ! 15.99940 + 1.008 for each H
 MASS CX10   13.01900 ! 12.01100 + 1.008 for each H

 autogenerate angles=true end

RESIdue HPP

GROUp
 ATOM  O1   TYPE OX1   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  C3   TYPE CX2   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C2   TYPE CX3   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  O2   TYPE OX9   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  C8   TYPE CX4   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C7   TYPE CX5   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  C6   TYPE CX4   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C5   TYPE CX10  CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C4   TYPE CX6   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  C9   TYPE CX10  CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C1   TYPE CX7   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  O3   TYPE OX8   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  O4   TYPE OX8   CHARge  0.0  END ! Nr of Hs =  0

 BOND  O1   C2       BOND  C3   C2       BOND  C3   C4       BOND  C2   C1
 BOND  O2   C7       BOND  C8   C7       BOND  C8   C9       BOND  C7   C6
 BOND  C6   C5       BOND  C5   C4       BOND  C4   C9       BOND  C1   O3
 BOND  C1   O4

 { edit these DIHEdrals if necessary }
 DIHEdral  C2   C3   C4   C5  ! flat ? (180 degrees = trans)   186.02
 DIHEdral  C2   C3   C4   C9  ! flat ? (0 degrees = cis)     6.04
 DIHEdral  C9   C8   C7   O2  ! flat ? (180 degrees = trans)   179.96
 DIHEdral  C9   C8   C7   C6  ! flat ? (0 degrees = cis)    -0.07
 DIHEdral  C7   C8   C9   C4  ! flat ? (0 degrees = cis)     0.10
 DIHEdral  O2   C7   C6   C5  ! flat ? (180 degrees = trans)   179.94
 DIHEdral  C8   C7   C6   C5  ! flat ? (0 degrees = cis)    -0.03
 DIHEdral  C7   C6   C5   C4  ! flat ? (0 degrees = cis)     0.09
 DIHEdral  C6   C5   C4   C3  ! flat ? (180 degrees = trans)   179.96
 DIHEdral  C6   C5   C4   C9  ! flat ? (0 degrees = cis)    -0.06
 DIHEdral  C3   C4   C9   C8  ! flat ? (180 degrees = trans)   179.94
 DIHEdral  C5   C4   C9   C8  ! flat ? (0 degrees = cis)    -0.04

 { edit these IMPRopers if necessary }
 IMPRoper  C2   O1   C3   C1  ! chirality or flatness improper     0.07
 IMPRoper  C7   O2   C8   C6  ! chirality or flatness improper     0.02
IMPRoper  C4   C3   C5   C9  ! chirality or flatness improper     0.01
 IMPRoper  C1   C2   O3   O4  ! chirality or flatness improper     0.05

 { edit these DONOrs and ACCEptors if necessary }
 ACCEptor  O1   C2
 ACCEptor  O2   C7
 ACCEptor  O3   C1
 ACCEptor  O4   C1

END { RESIdue HPP }

********************************************************************************
Remarks hpp.par
Remarks Created by XPLO2D V. 960804/2.1 at Wed Nov 4 10:28:52 1998 for user
jodi
Remarks Auto-generated by XPLO2D from file enol_o.pdb
Remarks Parameters for residue type HPP

 set echo=false end

 { edit if necessary }
 BOND OX1  CX3    1000.0  1.370 ! Nobs =    1
 BOND CX2  CX3    1000.0  1.350 ! Nobs =    1
 BOND CX2  CX6    1000.0  1.538 ! Nobs =    1
 BOND CX3  CX7    1000.0  1.530 ! Nobs =    1
 BOND OX9  CX5    1000.0  1.369 ! Nobs =    1
 BOND CX4  CX5    1000.0  1.389 ! Nobs =    2
 BOND CX4  CX10   1000.0  1.394 ! Nobs =    2
 BOND CX10 CX6    1000.0  1.402 ! Nobs =    2
 BOND CX7  OX8    1000.0  1.251 ! Nobs =    2

 { edit if necessary }
 ANGLe CX3  CX2  CX6    1000.0   137.84 ! Nobs =    1
 ANGLe OX1  CX3  CX2    1000.0   114.59 ! Nobs =    1
 ANGLe OX1  CX3  CX7    1000.0   109.67 ! Nobs =    1
 ANGLe CX2  CX3  CX7    1000.0   135.74 ! Nobs =    1
 ANGLe CX5  CX4  CX10   1000.0   119.95 ! Nobs =    2
 ANGLe OX9  CX5  CX4    1000.0   119.94 ! Nobs =    2
 ANGLe CX4  CX5  CX4    1000.0   120.12 ! Nobs =    1
 ANGLe CX4  CX10 CX6    1000.0   120.82 ! Nobs =    2
 ANGLe CX2  CX6  CX10   1000.0   120.83 ! Nobs =    2
 ANGLe CX10 CX6  CX10   1000.0   118.34 ! Nobs =    1
 ANGLe CX3  CX7  OX8    1000.0   119.63 ! Nobs =    2
 ANGLe OX8  CX7  OX8    1000.0   120.74 ! Nobs =    1

 { edit if necessary }
 DIHEdral CX3  CX2  CX6  CX10    750.0 0   90.000 ! Nobs =    2
! WARNING - large range for previous dihedral :    6.042 186.024
 DIHEdral CX10 CX4  CX5  OX9     750.0 0  180.000 ! Nobs =    2
 DIHEdral CX10 CX4  CX5  CX4     750.0 0    0.000 ! Nobs =    2
 DIHEdral CX5  CX4  CX10 CX6     750.0 0    0.000 ! Nobs =    2
 DIHEdral CX4  CX10 CX6  CX2     750.0 0  180.000 ! Nobs =    2
 DIHEdral CX4  CX10 CX6  CX10    750.0 0    0.000 ! Nobs =    2

 { edit if necessary }
 IMPRoper CX3  OX1  CX2  CX7     750.0 0    0.000 ! Nobs =    1
 IMPRoper CX5  OX9  CX4  CX4     750.0 0    0.000 ! Nobs =    1
 IMPRoper CX6  CX2  CX10 CX10    750.0 0    0.000 ! Nobs =    1
 IMPRoper CX7  CX3  OX8  OX8     750.0 0    0.000 ! Nobs =    1

 { edit if necessary }
 NONBonded OX1 0.1591 2.8509 0.1591 2.8509 ! assuming Oxygen
 NONBonded CX2 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
 NONBonded CX3 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
 NONBonded CX4 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
 NONBonded CX5 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
 NONBonded CX6 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
 NONBonded CX7 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
 NONBonded OX8 0.1591 2.8509 0.1591 2.8509 ! assuming Oxygen
 NONBonded OX9 0.1591 2.8509 0.1591 2.8509 ! assuming Oxygen
 NONBonded CX10 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon

 set echo=true end
********************************************************************************



More information about the X-plor mailing list