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1

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« on: December 30, 2025, 02:15:24 pm »

Thanks for sharing, Dr. Jun.
 I have downloaded the files, and I'll try to use this version with 3D-DART.
Kind regards.

2

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« on: December 30, 2025, 11:26:12 am »

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:

Code: [Select]

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

 I'd like to run some DNA simulations employing 3D-DART and I faced this same issue in my Linux. Could I receive one x3DNA version 2.15 to test in my DNA sequence?
Kind regards.