Good morning,
I believe I have encountered a bug of sorts in converting an Amber
trajectory to a GROMACS format...but it's unusual and perhaps very
limited in its inconvenience.
I converted an Amber trajectory to GROMACS style via cpptraj:
parm name_change.prmtop
trajin full_no_waters.mdcrd 49990 last 1
autoimage
trajout Equilibrated trr
go
quit
I can generate a .gro file via the ParmEd version being developed
currently by Jason Swails on github. When I visualize this in VMD, it
looks just fine. This is my only meaningful way to check that it works
correctly, and it passes just fine.
However, when I apply this trajectory to be analyzed using do_x3dna (a
software developed for analyzing GROMACS trajectories), it fails. After
consulting with the developer of the do_x3dna software, I find that he
confirms the trajectory is corrupt in some sense. I eventually tried
converting the trajectory via VMD, instead of cpptraj, and it worked
just fine in do_x3dna. The do_x3dna developer confirms using a
"normally" generated GROMACS .trr file (meaning not coming from Amber,
originally) works fine.
I do not mean to claim that the conversion in cpptraj does not work most
generally; it obviously worked fine for me when I checked it visually in
VMD. Moreover, I am sure this underwent more exhaustive testing that I
can appreciate. But in some quality, the conversion does not seem to work.
VMD works, but using a GUI is slow (I have many large trajectories). I
am going to begin experimenting with
http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion
by the esteemed Dr. Lemkul to find a way to do this on the command line.
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Wed Mar 16 2016 - 23:30:04 PDT
