[Chimera-users] Re: mdmovie/1508: instantaneous segmentation fault after clicking OK to multiple PDB molecular dynamics movie

Sabuj Pattanayek sabuj.pattanayek at vanderbilt.edu
Wed Mar 9 15:22:04 PST 2005


Thanks for looking into the problem. It would be nice to be able to read 
trr/xtc trajectories, but then would you also need to add functionality 
to read the gro file as well? Perhaps other Chimera users would also 
find these features useful.

Sabuj Pattanayek

Eric Pettersen wrote:

> Hi Sabuj,
>     I understand the problem now.  My code is not expecting the 
> individual PDB files to have MODEL/ENDMDL records in them (the code is 
> placing these records around each file as it collates them).  The 
> result is a mess.  I will work on making my code more robust in this 
> regard.
>     There is a fairly easy workaround for you though:  don't give the 
> -sep flag to trjconv.  You will get a single file containing the 
> frames bracketed by MODEL/ENDMDL records (which is what Chimera would 
> have had to assemble anyhow), which you can read by using the "single 
> file" option of the PDB format trajectory reader.  One caveat is that 
> the MD code expects the model numbers to start at 1, not 0, so you 
> will either have to renumber the MODEL records somehow, or delete 
> MODEL 0 from the file.  I will also work on handling files where the 
> numbering starts at zero.
>     Do you work with Gromacs trajectories a lot?  If you do, I could 
> put reading Gromacs trajectories directly on my to-do list.
> --Eric

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