[gmx-users] support mmcif format?
mailmd2011 at gmail.com
Mon Nov 23 14:49:50 CET 2015
probably there is some misunderstanding.
I didn't mean to store Gromacs trajectory to mmCIF format, but
extracting a specific snapshot from Gromacs trajectory into mmCIF file.
It is no doubt that the .xtc or .tng format is the best format for
Gromacs trajectory. However, when we use command:
trjconv -f md.xtc -s md.tpr -o test.pdb -sep -b xx -e xx
It will lead to many problems from the .PDB file if our system is too
big.... By contrast if it is mmCIF or PDBX format, everything would be
On 11/23/2015 12:08 PM, Hannes Loeffler wrote:
> It's hard to see for me why someone would even want to use mmCIF as
> a trajectory format. The format serves, primarily, the crystallography
> community to store a single set of coordinates together with a huge
> amount of meta data, most of which are probably rather irrelevant for
> trajectories. (For archiving purposes this is of course interesting
> but no need to write this into every single trajectory, just like the
> topology is kept separate).
> I think for the simulation community the mmCIF format should be what the
> PDB format should always have been: a read-only file format to be
> converted into a format developers think is best for their particular
> piece of software. Any future setup program should be able to read
> mmCIF but several libraries are already available to do exactly that.
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