The attached file "
x.out" has the following content:
handling file <struct_1_fixed.pdb>
Time used: 00:00:00:00
This structure has broken O3' to P[i+1] linkages
missing ' P ' atom : residue name 'THY', chain B, number [ 27 ]
missing ' OP1' atom : residue name 'THY', chain B, number [ 27 ]
missing ' OP2' atom : residue name 'THY', chain B, number [ 27 ]
missing ' P ' atom : residue name 'THY', chain B, number [ 1 ]
missing ' P ' atom : residue name 'THY', chain B, number [ 27 ]
This means 3DNA v2.4.4 itself is running properly.
However, the file also contains "
EnergyPDNA.exe: command not found". EnergyPDNA.exe is not part of 3DNA, v1.5 or v2.x. It could be part of 3D-DART.
From 3DNA v1.5 to v2.x, there is indeed reorganization of data folders, including:
BASEPARS ---> config
Examples ---> examples
FIBER ---> fiber
The most important one is
BASEPARS ---> config.
For your convenience, I have dug out 3DNA v1.5, and sent you an email with links for download.
Note that 3DNA v1.5 is no longer supported. Even 3DNA v2.x is under maintenance mode: no more new features, only bug fixes. All new developments are devoted to DSSR and SNAP, which supersede 3DNA.
Best regards,
Xiang-Jun