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Dear 3DNA community,
I would like to ask you a question about Curves+ program.
I perform my simulations using NAMD package. It works with files in CHARMM format. I.e. it uses topology files in .psf extension and calculates trajectory files in .dcd extension.
Curves+ is working with input files in AMBER format.
Is there any possibility to analyse in Curves+ trajectories calculated by NAMD? Maybe there are some programs that can convert files from CHARMM to AMBER format?
Thank you in advance.
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Since these are a Curves+ (https://bisi.ibcp.fr/tools/curves_plus/)-specific questions, you may have a better chance to get them answered from the Curves+ user community.
I understand that each MD package has a unique native format. However, each MD package should (I believe) have a method to convert its native format to the standard NMR-like MODEL/ENDMDL ensemble format, as in the PDB.
As far as 3DNA goes, the find_pair -curve+ option handles a single structure in PDB format (e.g., find_pair -curve+ 355d.pdb). It aims to simplify the preparation step to the Curves+ program.
HTH,
Xiang-Jun
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.