[gmx-users] Re: Re: trjconv and missing chain identifier
mark.abraham at anu.edu.au
Mon Mar 5 13:05:46 CET 2007
> 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
> VMD can unfortunately not do what I need so is there no way to get the
> chain identifier like in the first example?
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