[gmx-users] Re: Re: trjconv and missing chain identifier

[Mark Abraham]

> Mark
>
> Hi Mark and other users,
>
> Thanks for your reply and apologies for my English.
>
> If the chain identifiers are  discarded by gromacs why do I than get
> from trjconv an output file looking like this when having more than one
> chain in the .trr file like in this example (part of .pdb file)
>
> ATOM   2776  O1  PHE A 336      32.109  64.621  29.258  1.00  0.00
> ATOM   2777  O2  PHE A 336      30.372  64.241  30.505  1.00  0.00
> ATOM   2778  N   THR B 337      60.139  23.423  46.095  1.00  0.00
> ATOM   2779  CA  THR B 337      58.765  23.151  45.661  1.00  0.00
>
> but not when I have only one chain in the .trr like in this example
> (part of .pdb file).
>
> ATOM   2776  O1  PHE   336      41.051  55.857  23.785  1.00  0.00
> ATOM   2777  O2  PHE   336      42.809  56.115  22.532  1.00  0.00

That surprises me, maybe I've misunderstood something about how this all
works. Certainly the .gro/.g96 formats do not have chain identifiers, so
one possiblity was that the first .trr was generated from an grompp -c
struct.pdb and the second from grompp -c struct.gro (or maybe mdrun -c
similarly).

> VMD can unfortunately not do what I need so is there no way to get the
> chain   identifier like in the first example?

Mark