[gmx-developers] trjconv & pdb_use_ter?

[Anton Feenstra]

Berk Hess wrote:
> 
> That was really a long time ago, so I don't really remember.
> All Gromacs pdb files and nmr pdb files have ENDMDL's.
> You can easily fix other files by replacing all TER's by ENDMDL.
> It is better to keep the alreay huge amount of options of trjconv to a
> minimum, but if you really need it you can add it.

Yeah, I know -- 29 options... :-/
It's simply very convenient when you're analyzing loads of sets of 
.pdb files. I've been doing it with the TER->ENDMDL replacement up 
to now but that just slows things down a bit too much, IMO.

> The TPS option for trjconv is fine with me, but ideally there should be a common
> routine for all gromacs programs which reads a trajectory and optionally a tps
> and an index file, so this can be done automatically for all programs and more
> importantly the consistency of the input files can be checked.

OK, that is something for another time. 
In the meantime I'll add the 'hand-coded' version to trjconv.

> PS Don't forget to add the -fitall option back to g_rms, which should be
> turned on by default.

Yes, I merged it into the -fit enum option, but I realise now that is 
not what you want. I've put the original -fitall hidden option back in
and removed it from the -fit enum.

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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