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Check in on March 20, 2013 by Junmei Wang
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1. antechamber.c
        changed the default_flag option for some formats. The purpose is to
        aviod using atom names as AMBER atom types for formats like ac, prepi and prepc
        added new option to read in radius parameters using -a flag
        gaussian version keyword (-gv) is replaced with a flag of whether generating gesp file 

        The early Guassian 09 sub-version cannot produce ESP and therefore we introduced 
        gesp file. Later on, the Gaussian 09 subversions can produce ESP again (as the 
        previous Gaussian versions, g03 and g98 do)  

2-3. gzmat.c and gcrt.c
        added code to provide default radius parameters, such as I, which are missing in Gaussian
        added code to use proper basis set. Three basis sets are used based on the element information:
        6-31G*, CEP-31G and SDD
        The radius and basis set information is in $AMBERHOME/dat/antechamber/ESPPARM.DAT

4. charge.c
        added code to read ESP charges from Gaussian output whenever possible. Otherwise, Mulliken
        atomic charges are read.

5. espgen.c
        improved code to extract ESP from both Gaussian log and gesp files

6. respgen.c
        improved code to generate inputs for both resp and i_resp fitting

7-8. common.c and atom.h
        changed to reflect the changes on antechamber.c and gzmat.c/gcrt.c

9. parmchk.c
        added new function to read frcmod file

10. parmchk2.c
        developed a new program to calculate or search the substitute for missing FF parameters.
        parmchk2 finds the best substitution based on parameters on $AMBERHOME/dat/antechamber/PARMCHK.DAT
        parmchk will be replaced withparmchk2 in the next AMBER release?
        More details on algorithm will be provided in the manual

11. rotate.c
        add a new function to list all the atoms linking to two atoms through covalent bonds

12. jout.c 
        correct a comment line

13. prepgen.c
        modify some numbers to hopefully better deal with the collinear problem 

14. gaff.dat
        I have reoptimized X -c -ca-X parameter using modle compound of acetophenone
        I found force constant of 4.0 gives almost identical result to ab initio at MP2/aug-cc-pVTZ level
        for the 18 relative energies (rms error = 0.04 kcal/mol)
        The original value, 14.5, which is inherited from AMBER protein force field is too large
        On the other hand, Hao's value (1.5), recommended by Romain is too small.
	Similarily, the force constant of X -c2-ca-X has been changed to  2.800. 
	New force field parameters:

	X -c -ca-X    4    4.000       180.000           2.000      optimized by Junmei Wang, Jan-2013
	X -c2-ca-X    4    2.800       180.000           2.000      optimized by Junmei Wang, March 2013

15. ATCOR.DAT
        added correspondence for newly introduced atom types

16. Makefile
        revised to deal with parmchk2.c

Newly introduced Files
        parmchk2.c
        PARMCHK.DAT
        ESPPARM.DAT