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

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Date: 08.11.04 - 10.11.04
Author: Klvana, M.

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Motivation: 

•	Preparation of PDB and PREP files of R-DCL for molecular docking (PDB), molecular mechanics and dynamics AMBER (PDB and PREP) since R-DCL is the major product of 1,2,3-trichloropropane (TCP) dehalogenation by DhaA.

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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 R-DCL was prepared in PYMOL from PDB structure of TCP. Atoms were re-ordered and renumbered according to the PDB file of TCP. R-DCL was energetically minimised using GAUSSIAN (RHF/6-31G*). The geometrically optimised structure was used as final geometry of R-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 R-DCL (R-DCL.pdb):
COMPND    (R)-2,3-dichloro-1-propanol
AUTHOR    Klvana, M. 09.11.04
ATOM      1  C1  DCL     1      -0.594   1.237   0.388  1.00         0.160044
ATOM      2  O2  DCL     1      -1.688   1.860  -0.205  1.00        -0.641457
ATOM      3  H3  DCL     1      -2.477   1.366  -0.023  1.00         0.419728
ATOM      4  H4  DCL     1      -0.744   1.087   1.454  1.00         0.051498
ATOM      5  H5  DCL     1       0.246   1.903   0.255  1.00         0.107286
ATOM      6  C6  DCL     1      -0.260  -0.097  -0.272  1.00        -0.026626
ATOM      7 Cl7  DCL     1      -1.645  -1.241  -0.027  1.00        -0.200509
ATOM      8  H8  DCL     1      -0.178   0.032  -1.339  1.00         0.175097
ATOM      9  C9  DCL     1       0.977  -0.784   0.288  1.00        -0.222859
ATOM     10 Cl10 DCL     1       2.462   0.137  -0.111  1.00        -0.166170
ATOM     11  H11 DCL     1       0.928  -0.869   1.362  1.00         0.164341
ATOM     12  H12 DCL     1       1.096  -1.764  -0.142  1.00         0.179626
TER

•	PREP file of R-DCL (R-DCL.prp):
0    0    2

(R)-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   5.7630   0.0000   0.0000    0.000000
   3   DU   DU    M   2   1   0   3.6180  90.0000 -90.0000    0.000000
   4   C1   CT    M   3   2   1   4.4330  90.0000 270.0000    0.160044
   5   O2   OH    S   4   3   2   1.4298 113.9312 197.2703   -0.641457
   6   H3   HO    E   5   4   3   0.9600 109.5212 227.2052    0.419728
   7   H4   H1    E   4   3   2   1.1168  19.4548 124.3737    0.051498
   8   H5   H1    E   4   3   2   1.1193  90.3071 305.6924    0.107286
   9   C6   CT    M   4   3   2   1.5153 120.8048  59.1193   -0.026626
  10  Cl7   CL    E   9   4   3   1.7666 110.6489  70.5829   -0.200509
  11   H8   H1    E   9   4   3   1.1223 110.6210 186.9335    0.175097
  12   C9   CT    M   9   4   3   1.5173 111.0936 310.1888   -0.222859
  13 Cl10   CL    E  12   9   4   1.7537 111.5452 288.3385   -0.166170
  14  H11   H1    E  12   9   4   1.1164 111.1932  47.6683    0.164341
  15  H12   H1    E  12   9   4   1.1177 110.7882 170.0077    0.179626

DONE
STOP

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Conclusions:

•	PDB (R-DCL.pdb) and PREP (R-DCL.prp) files of R-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:

•	R-DCL.pdb and R-DCL.prp:
	klvanamn@cronus:/home/klvanamn/DATA/STR/LIG/PDB
	klvanamn@cronus:/home/klvanamn/DATA/STR/LIG/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 R-DCL:
	klvanamn@cronus:/home/klvanamn/DATA/STR/LIG/PAR/R-DCL
	martink@eldar.chemi.muni.cz:/home/data/martink/STR/LIG/PAR/R-DCL
            (PAR = Parametrization)