[gmx-users] Extracting the last frame of simulation into PDB

zugunder schlecht at mail.ru
Fri Feb 15 20:08:55 CET 2013


I bumped into a small problem, I think I missed something... so I am asking
for help.

I made a simulation of a protein in water (35ns, extended 3 times from
initial 10ns) and now I need to get a resulting protein structure in pdb.
So I issued:

g_trjconv -s md_input_extended_to35ns.tpr -f md_product.xtc -o
md_product_35ns.pdb -dump 34999

But the resulting pdb looks weird when I open it in VMD or Chimera - it
looks like the structure is split into 2 parts (within one file) and I can
see several huge gaps in coordinates when viewing the file content. Gromacs
trjconv manual doesn't seem to describe this behaviour, so could I ask
anyone to help me with this?

Thank you.

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