Index of /~chem/chemistry/software/heme

 Name                    Last modified       Size  Description

 Parent Directory        29-Jun-2004 09:10      -  
 README                  30-Sep-2003 20:12     2k  
 benzene.eng             30-Sep-2003 20:12     1k  
 benzene.g94             30-Sep-2003 20:12     1k  
 benzene.p94             30-Sep-2003 20:12     1k  
 benzene.pdb             30-Sep-2003 20:12     1k  
 benzene.prep            30-Sep-2003 20:12     3k  
 benzene.vib             30-Sep-2003 20:12     1k  
 ethben.g94              30-Sep-2003 20:12     2k  
 ethben.p94              30-Sep-2003 20:12     2k  
 ethben.pdb              30-Sep-2003 20:12     1k  
 ethben.prep             30-Sep-2003 20:12     3k  
 ethben.vib              30-Sep-2003 20:12     2k  
 heme.readme             30-Sep-2003 20:12     2k  
 heme_his.pdb            30-Sep-2003 20:12     6k  
 heme_his.prep           30-Sep-2003 20:12    15k  
 heme_his_co.pdb         30-Sep-2003 20:12     6k  
 heme_his_co.prep        30-Sep-2003 20:12    11k  
 heme_his_co.vib         30-Sep-2003 20:12     7k  
 parm_heme.dat           30-Sep-2003 20:12    36k  
 pyridine.g94            30-Sep-2003 20:12     1k  
 pyridine.p94            30-Sep-2003 20:12     1k  
 pyridine.pdb            30-Sep-2003 20:12     1k  
 pyridine.prep           30-Sep-2003 20:12     3k  
 pyridine.vib            30-Sep-2003 20:12     1k  
 pyrrole.eng             30-Sep-2003 20:12     2k  
 pyrrole.g94             30-Sep-2003 20:12     2k  
 pyrrole.p94             30-Sep-2003 20:12     2k  
 pyrrole.pdb             30-Sep-2003 20:12     1k  
 pyrrole.prep            30-Sep-2003 20:12     2k  
 pyrrole.vib             30-Sep-2003 20:12     2k  
 styrene.p94             30-Sep-2003 20:12     2k  
 styrene.pdb             30-Sep-2003 20:12     1k  
 styrene.prep            30-Sep-2003 20:12     3k  
 styrene.vib             30-Sep-2003 20:12     2k  
 toluene.p94             30-Sep-2003 20:12     2k  
 toluene.pdb             30-Sep-2003 20:12     1k  
 toluene.prep            30-Sep-2003 20:12     3k  
 toluene.vib             30-Sep-2003 20:12     2k  

This directory contains AMBER force field parameters developed in our
laboratory. The following extensions have been used:

        .pdb  coordinate file used for edit -pi input
        .prep prep file used for prep -i input
        .g94, .p94, .eng, and .vib are force field input for parm -m

The force fields have been optomized in different ways:

        .g94 correctly fits the energy of distortion of these molecules as 
             calculated from a Gaussian 94 calculation
        .p94 is the original AMBER parm94 data set
        .vib is the best fit to the normal mode of vibration of these molecules
        .eng is the best fit to both energies of distortion and experimental
             vibration data. When available this represents the most balanced
             force field.

The following new atom types have been defined:

        NO,NP   porphyrin nitrogens
        ND      pyridine nitrogen
        NE      pyrrole nitrogen

        CD      meso carbon in porphyrin
        CE      alpha carbon in porphyrin
        CF      beta carbon in porphyrin
	CG	carbons next to nitrogens in pyrrole and pyrridine (like CQ or CW)
	CH	beta carbon in pyrrole
	CI	benzene carbon with a carbon substituent (like CA)
	CJ	vinyl carbon (like CM)

	HN	pyrrole hydrogen
	HM	methane hydrogen
	HJ	vinyl hydrogen
	HK	vinyl hydrogen

The following atom types have been modified:

	CA	benzene carbon
	CT	any sp3 carbon
	HC	ethane like hydrogens

The following atom types have been used but not modified:

	H 	nitrogen hydrogen
	HA 	benzene hydrogen

The following force fields are included.

        Benzene
        Pyrrole
        Pyridine
        Pyridine ligand (pyridinel)
        Toluene
        Ethylbenzene (ethben)
        Styrene
        Nickel octaethyl porphine (nioep) in progress
        protoporphyrin IX attached to histidine (heme_his) in progress
        protoporphyrin IX attached to his & CO (heme_his_co) in progress
        protoporphyrin IX in parm.dat format   parm_heme.dat in progress