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Questions and answers => General discussions (Q&As) => Topic started by: alxdorev on March 06, 2017, 10:54:31 am

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Title: Using Curves+ with NAMD
Post by: alxdorev 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.

Title: Re: Using Curves+ with NAMD
Post by: xiangjun on March 06, 2017, 12:10:07 pm

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


 

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Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University