---------- Forwarded message ----------
Date: Fri, 8 Jan 1999 09:02:56 -0500 (EST)
From: Jeannie Rojas <jrojas at crystal.wistar.upenn.edu>
To: x-plor at net.bio.net
Subject: Acetylated Lysine in XPLOR
Hello,
I am trying to incorporate an acelylated lysine residue into my protein. I
used XPLO2D to auto generate the topology file:
-----------------------------------------------------------------------
Remarks aly.top Remarks Created by XPLO2D V. 961213/2.2.1 at Thu Jan 7
09:28:32 1999 for user jrojas Remarks Auto-generated by XPLO2D from file
aly.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 NX1 16.02270 ! 14.00670 + 1.008 for each H
MASS CX2 13.01900 ! 12.01100 + 1.008 for each H
MASS CX3 14.02700 ! 12.01100 + 1.008 for each H
MASS CX4 14.02700 ! 12.01100 + 1.008 for each H
MASS NX5 14.00670 ! 14.00670 + 1.008 for each H
MASS CX6 13.01900 ! 12.01100 + 1.008 for each H
MASS OX7 15.99940 ! 15.99940 + 1.008 for each H
MASS CX8 12.01100 ! 12.01100 + 1.008 for each H
MASS CX9 13.01900 ! 12.01100 + 1.008 for each H
MASS CX10 14.02700 ! 12.01100 + 1.008 for each H
MASS CX11 14.02700 ! 12.01100 + 1.008 for each H
MASS OX12 15.99940 ! 15.99940 + 1.008 for each H
autogenerate angles=true end
RESIdue ALY
GROUp
ATOM N TYPE NX1 CHARge 0.0 END ! Nr of Hs = 2
ATOM CA TYPE CX2 CHARge 0.0 END ! Nr of Hs = 1
ATOM CB TYPE CX3 CHARge 0.0 END ! Nr of Hs = 2
ATOM CG TYPE CX10 CHARge 0.0 END ! Nr of Hs = 2
ATOM CD TYPE CX11 CHARge 0.0 END ! Nr of Hs = 2
ATOM CE TYPE CX4 CHARge 0.0 END ! Nr of Hs = 2
ATOM NZ TYPE NX5 CHARge 0.0 END ! Nr of Hs = 0
ATOM C TYPE CX6 CHARge 0.0 END ! Nr of Hs = 1
ATOM O TYPE OX7 CHARge 0.0 END ! Nr of Hs = 0
ATOM CX TYPE CX8 CHARge 0.0 END ! Nr of Hs = 0
ATOM OX1 TYPE OX12 CHARge 0.0 END ! Nr of Hs = 0
ATOM CX1 TYPE CX9 CHARge 0.0 END ! Nr of Hs = 1
BOND N CA BOND CA CB BOND CA C BOND CB CG
BOND CG CD BOND CD CE BOND CE NZ BOND NZ CX
BOND C O BOND CX OX1 BOND CX CX1
{ edit these DIHEdrals if necessary }
DIHEdral CA CB CG CD ! flat ? (180 degrees = trans) 185.31 ! DIHEdral CB
CG CD CE ! perhaps a fixed dihedral ??? -85.12 ! DIHEdral CG CD CE NZ !
perhaps a fixed dihedral ??? -59.99 ! DIHEdral CD CE NZ CX ! perhaps a
fixed dihedral ??? -87.86
{ edit these IMPRopers if necessary }
IMPRoper CA C CB N ! chirality or flatness improper 33.56
IMPRoper CX NZ OX1 CX1 ! chirality or flatness improper 0.06
{ edit these DONOrs and ACCEptors if necessary } ! DONOr H?1 N ! DONOr
H?2 N
ACCEptor O C
ACCEptor OX1 CX
END { RESIdue ALY }
--------------------------------------------------------------------------
and the parameter file :
Remarks aly.par Remarks Created by XPLO2D V. 961213/2.2.1 at Thu Jan 7
09:28:35 1999 for user jrojas Remarks Auto-generated by XPLO2D from file
aly.pdb Remarks Parameters for residue type ALY
set echo=false end
{ edit if necessary }
BOND NX1 CX2 1000.0 1.465 ! Nobs = 1
BOND CX2 CX3 1000.0 1.537 ! Nobs = 1
BOND CX2 CX6 1000.0 1.512 ! Nobs = 1
BOND CX3 CX10 1000.0 1.528 ! Nobs = 1
BOND CX10 CX11 1000.0 1.530 ! Nobs = 1
BOND CX11 CX4 1000.0 1.520 ! Nobs = 1
BOND CX4 NX5 1000.0 1.460 ! Nobs = 1
BOND NX5 CX8 1000.0 1.335 ! Nobs = 1
BOND CX6 OX7 1000.0 1.238 ! Nobs = 1
BOND CX8 OX12 1000.0 1.254 ! Nobs = 1
BOND CX8 CX9 1000.0 1.244 ! Nobs = 1
{ edit if necessary }
ANGLe NX1 CX2 CX3 500.0 108.75 ! Nobs = 1
ANGLe NX1 CX2 CX6 500.0 112.32 ! Nobs = 1
ANGLe CX3 CX2 CX6 500.0 108.05 ! Nobs = 1
ANGLe CX2 CX3 CX10 500.0 114.06 ! Nobs = 1
ANGLe CX3 CX10 CX11 500.0 112.02 ! Nobs = 1
ANGLe CX10 CX11 CX4 500.0 113.16 ! Nobs = 1
ANGLe CX11 CX4 NX5 500.0 113.60 ! Nobs = 1
ANGLe CX4 NX5 CX8 500.0 125.17 ! Nobs = 1
ANGLe CX2 CX6 OX7 500.0 121.34 ! Nobs = 1
ANGLe NX5 CX8 OX12 500.0 121.99 ! Nobs = 1
ANGLe NX5 CX8 CX9 500.0 120.63 ! Nobs = 1
ANGLe OX12 CX8 CX9 500.0 117.37 ! Nobs = 1
{ edit if necessary }
DIHEdral CX2 CX3 CX10 CX11 750.0 0 180.000 ! Nobs = 1
DIHEdral CX3 CX10 CX11 CX4 750.0 0 -90.000 ! Nobs = 1
DIHEdral CX10 CX11 CX4 NX5 750.0 0 -60.000 ! Nobs = 1
DIHEdral CX11 CX4 NX5 CX8 750.0 0 -90.000 ! Nobs = 1
{ edit if necessary }
IMPRoper CX2 CX6 CX3 NX1 750.0 0 35.000 ! Nobs = 1
IMPRoper CX8 NX5 OX12 CX9 750.0 0 0.000 ! Nobs = 1
{ edit if necessary }
NONBonded NX1 0.2384 2.8509 0.2384 2.8509 ! assuming Nitrogen
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 NX5 0.2384 2.8509 0.2384 2.8509 ! assuming Nitrogen
NONBonded CX6 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
NONBonded OX7 0.1591 2.8509 0.1591 2.8509 ! assuming Oxygen
NONBonded CX8 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
NONBonded CX9 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
NONBonded CX10 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
NONBonded CX11 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
NONBonded OX12 0.1591 2.8509 0.1591 2.8509 ! assuming Oxygen
set echo=true end
-----------------------------------------------------------
These work fine in generate.inp, but when I use check.inp I get the
following error message:
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId="PROC", RESId="313 ", NAME="C ", CHEMical="C "
ATOM2: SEGId="PROC", RESId="314 ", NAME="N ", CHEMical="NX1 "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId="PROC", RESId="314 ", NAME="C ", CHEMical="CX6 "
ATOM2: SEGId="PROC", RESId="315 ", NAME="N ", CHEMical="NH1 "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODBON-ERR: program will be aborted.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
Can anyone offer some suggestion. It seems that this new acetylated
lysine is not patching with the residues on either side of it based on the
error message above.
Jeannie Rojas
jrojas at crystal.wistar.upenn.edu
