Ever wondered how you might translate trajectories from one Molecular Dynamics package to another? It's a thorny little problem that's afflicted quite a few structural biologists. Here's one ugly solution that I am rather proud of.
A Most Ugly Hack: translating from CHARMM to AMBER trajectories
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Simulaid
I have no idea about converting trajectories, but people talk about using Simulaid [ http://inka.mssm.edu/~mezei/simulaid/ ] for similar stuff, did you check it?
simulaid
I downloaded it but couldn't get it to work properly for NAMD to AMBER.
Looks familiar
Good to see that file format conversion is a full-time preoccupation in structural biology as well as for people working with sequences. Nice how-to.
Just a wild guess, but I'm
Just a wild guess, but I'm thinking this particular piece will not have the same broad impact of "Notes to a young computational biologist". Nonetheless, I am thinking that maybe your posts on these topics have brought a few more structural biologists into the world of blogging :)
Nightmares
And I shudder at the memories of trajectory formats.
We should start a movement for MD standards, as in Force Field standards, trajectories, etc etc.