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Questions and answers => MD simulations => Topic started by: temizna on March 10, 2011, 10:50:17 am

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Title: Snapshots must be separated by MODEL/ENDMDL
Post by: temizna on March 10, 2011, 10:50:17 am

Dear Xiang-Jun,
I have just noticed another potential bug. Your ruby script looks only MODEL/ENDMDL pairs to separate each snapshot. Although this works for the sample trajectory pdb you use (which was created using gromacs), not every visualization/simulation package create the files same way. For example, vmd does not use MODEL to start each snapshot and it ends with END only. Some other programs use TER instead of END. May be we should start matching "ATOM     1 " assuming there is always a first atom from the simulation trajectory.

HTH,
Alpay

Title: Re: Ruby scripts for the analysis of MD simulation trajector
Post by: xiangjun on March 10, 2011, 09:29:42 pm

Hi Alpay,

Thanks for the info. Clearly (but not surprisingly), there are many variants of ensemble-format from different visualization/simulation packages. It is impractical nor desirable for the Ruby scripts to account for each and every such possibility. By design, the scripts deal only the simplest/commonest case where each model/snapshot is delineated by the MODEL/ENDMDL pair, and are directly applicable to the analysis of NMR ensembles from the PDB/NDB. To make this point even clearer, I have added  the following sentence to the release post (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=11&t=195):

Quote

Importantly, for the [mono:2fyxsqwq]-e[/mono:2fyxsqwq] and [mono:2fyxsqwq]-m[/mono:2fyxsqwq] options, each model in the ensemble must be delimited by an MODEL/ENDMDL pair, as clearly documented in the Coordinate Section of the PDB format (http://http://www.wwpdb.org/documentation/format32/sect9.html).

The commonly used ensemble formats are better and easily handled on a case-by-case basis, with the following three choices:

• Ask the original software package creator/maintainer to provide support for the MODEL/ENDMDL format, as it is well-documented in the PDB format.
• Write a purpose-specified script to perform the conversion as needed by the user.
• As time permits and with responsive and knowledgeable collaborators, I will consider to write and integrate conversion scripts into the distribution.

Note that starting with v0.1, the scripts support four options ([mono:2fyxsqwq]-e, -m, -p, -l[/mono:2fyxsqwq]) to allow great flexibility.

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.