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Author Topic: Using Curves+ with NAMD  (Read 459 times)

Offline alxdorev

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Using Curves+ with NAMD
« on: March 06, 2017, 10:54:31 am »
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.

Offline xiangjun

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Re: Using Curves+ with NAMD
« Reply #1 on: March 06, 2017, 12:10:07 pm »
Since these are a Curves+-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


 
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.