nodalpoint.org - A Most Ugly Hack: translating from CHARMM to AMBER trajectories - Comments

simulaid

bosco — Thu, 16 Aug 2007 13:23:16 -0400

I downloaded it but couldn't get it to work properly for NAMD to AMBER.

Simulaid

Animesh — Thu, 16 Aug 2007 10:46:02 -0400

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?

Looks familiar

Neil — Wed, 15 Aug 2007 09:52:19 -0400

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

Greg — Tue, 14 Aug 2007 14:11:00 -0400

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

mndoci — Tue, 14 Aug 2007 14:09:44 -0400

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.

A Most Ugly Hack: translating from CHARMM to AMBER trajectories

bosco — Mon, 13 Aug 2007 01:48:49 -0400

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.