Parametrization of 2,3-dichloro-1-propanol (DCL) for AMBER Force Field

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Date: 04.10.04 - 06.10.04
Author: Klvana, M.

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Motivation: 

•	Preparation of PDB and PREP files of DCL for molecular docking (PDB), molecular mechanics and dynamics AMBER (PDB and PREP).

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Methods:

•	List of Programmes and Scripts: BABEL 1.6 (University of Arizona, Tucson, USA), PYMOL 0.97 (DeLano Scientific, San Diego, USA), MOPAC 2000 (Fujitsu, Tokyo, Japan), GAUSSIAN 94 (Gaussian, Inc., Pittsburgh, USA), AMBER 5 (University of Carolina, San Francisco, USA), fgpdb2z_eng, gresp, greadit and readit;

•	Procedure: Initial PDB file of DCL was prepared in PYMOL from PDB structure of 1,2,3-trichloropropane (TCP). Atoms were re-ordered and renumbered according to the PDB file of TCP. DCL was energetically minimised using GAUSSIAN (RHF/6-31G*). The geometrically optimised structure was used as final geometry of DCL and for recalculation of molecular electrostatic potentials (MEPs) by GAUSSIAN (6-31G*). The MEPs were extracted from GAUSSIAN output by the scripts gresp, greadit and readit, and fitted at molecular surface as partial atomic charges using RESP methodology (AMBER). The charges were pasted into PDB and PREP file. The latter one was prepared by addition of dummy atoms and conversion to z-matrix format of coordinates using the script fgpdb2z_eng.

Results:

•	PDB file of DCL (mDCL.pdb):
COMPND    mDCL.pdb - 2,3-dichloro-1-propanol 
AUTHOR    Klvana, M. 06.10.04
ATOM      1  C1  DCL     1      -1.889  -0.174   0.123  1.00   0.132646
ATOM      2  O2  DCL     1      -2.142  -1.512  -0.206  1.00  -0.631879
ATOM      3  H3  DCL     1      -3.041  -1.730  -0.004  1.00   0.434142
ATOM      4  H4  DCL     1      -2.021   0.006   1.187  1.00   0.064595
ATOM      5  H5  DCL     1      -2.544   0.497  -0.420  1.00   0.057884
ATOM      6  C6  DCL     1      -0.445   0.115  -0.274  1.00  -0.089823
ATOM      7 Cl7  DCL     1      -0.130   1.860   0.012  1.00  -0.175373
ATOM      8  H8  DCL     1      -0.325  -0.048  -1.334  1.00   0.211077
ATOM      9  C9  DCL     1       0.526  -0.755   0.503  1.00  -0.205074
ATOM     10 Cl10 DCL     1       2.197  -0.653  -0.120  1.00  -0.165503
ATOM     11  H11 DCL     1       0.220  -1.784   0.412  1.00   0.182763
ATOM     12  H12 DCL     1       0.554  -0.474   1.544  1.00   0.184546
TER

•	PREP file of DCL (mDCL.prp):
0    0    2
2,3-dichloro-1-propanol
dcl.data
DCL INT 1
CORRECT OMIT DU BEG
0.0
   1   DU   DU    M   0  -1  -2   0.0000   0.0000   0.0000   0.000000
   2   DU   DU    M   1   0  -1   9.3970   0.0000   0.0000   0.000000
   3   DU   DU    M   2   1   0   3.5410  90.0000 -90.0000   0.000000
   4   C1   CT    M   3   2   1   9.7040  90.0000 270.0000   0.132646
   5   O2   OH    S   4   3   2   1.4302 104.9931 309.8905  -0.631879
   6   H3   HO    E   5   4   3   0.9602 109.5025 349.6068   0.434142
   7   H4   H1    E   4   3   2   1.1164   3.7841  71.8110   0.064595
   8   H5   H1    E   4   3   2   1.1177 113.5168  65.6856   0.057884
   9   C6   CT    M   4   3   2   1.5173 109.4400 190.0219  -0.089823
  10  Cl7   CL    E   9   4   3   1.7666 108.3491 282.3464  -0.175373
  11   H8   H1    E   9   4   3   1.1223 110.6156 167.3505   0.211077
  12   C9   CT    M   9   4   3   1.5153 111.0936  44.0921  -0.205074
  13 Cl10   CL    E  12   9   4   1.7484 112.1702 171.3585  -0.165503
  14  H11   H1    E  12   9   4   1.1193 109.7999  52.9736   0.182763
  15  H12   H1    E  12   9   4   1.1168 111.2924 291.2450   0.184546

DONE
STOP

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Conclusions:

•	PDB (mDCL.pdb) and PREP (mDCL.prp) files of DCL are compatible one to each other. The files can be used for planned molecular docking, molecular mechanics and molecular dynamics calculations.

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Data:

•	mDCL.pdb and mDCL.prp:
	martink@eldar.chemi.muni.cz:/home/data/martink/STR/LIG/PDB
	martink@eldar.chemi.muni.cz:/home/data/martink/STR/LIG/PRP
            (STR = Structures, LIG = Ligands)

•	Parametrization of DCL:
	martink@eldar.chemi.muni.cz:/home/data/martink/STR/LIG/PAR/DCL
            (PAR = Parametrization)