#Running:
bash-3.00$: export DATADIR=""; ./dDFIRE pro.pdb
pro.pdb: -689.14	 -510.871 -96.3454 -53.5374 -28.3821
##
Attn: dDFIRE include 4 terms: one is distance-related only, i.e. DFIRE2; the other 3 are angles related.
In the above output, -689.14 is the total energy, and the following are DFIRE, and 3 angle-related terms in dDFIRE.
#
In default, it's dDFIRE. For distance-only DFIRE part, the potential is sysmmetric.
"-nosym" option is to set asymmetric DFIRE (aDFIRE)
"-noag" option is to close the angle related terms
"-V" DEBUG mode
# Tips:
1. The program can be followed with many PDB files. The pdb should include all atoms.

2. The enviornment variable "DATADIR" is used, where two files "amino.dat" and "dfire.1" are read. If not set, the default searching path is the current directory.

3. The program is compiled on X86-linux with Intel C compiler; both 32bit & 64 bit should be ok.

4. dDFIRE_pair has one option "-pair" to print residue-pair interaction energy

#References
1. Yuedong Yang and Yaoqi Zhou, Specific interactions for  ab initio folding of protein terminal regions with secondary structures. Proteins 72, 793-803 (2008)
2. Yuedong Yang and Yaoqi Zhou, Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely-related all-atom statistical energy functions. Protein Science 17 1212-1219, (2008)


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**If you have any more questions, please feel free to contact me: yuedong.yang@gmail.com

Last updated on May 13, 2010
