Dear Amber Users,
I have .mdcrd and .prmtop files that I am trying to use to generate a
.pdb output file that x3DNA plays nicely with. The trajectory is a 20 bp
DNA solvated in tleap by the solvateoct command. If I visualize the
.mdcrd file, everything looks just fine. I use the following ptraj
script to try to generate the .pdb file I need for subsequent analysis:
trajin md2.mdcrd 1000 19000 5
strip :WAT
strip :Na+
unwrap :1-40
center :1-40 mass origin
image origin center familiar
trajout output.pdb pdb append
The resulting .pdb file looks great for the first few thousand
simulation frames (i.e. frames 1000 to almost 5000 from the simulation
convert just fine) while the latter 75% of the frames produce .pdb
structures that look like a cubic periodic box that has exploded. The
energies and .mdcrd file look fine so an explosion is clearly not the
explanation. Am I missing something in my ptraj input file above to
properly deal with the non-cubic periodic box the simulation was run
with? Does anyone have a script they have successfully used to do this
conversion? I could easily generate the pdb using VMD and the
correct-looking mdcrd file and then write a script to add the MODEL and
ENDMDL flags 3DNA looks for but I'd rather get my ptraj script working
properly.
FYI, using the same script above without the lines "unwrap :1-40\ center
:1-40 mass origin\ image origin center familiar\" also produces the same
strange output.
Thanks in advance for this and all the other help this listserve and the
developers have provided over the years.
-Gordon
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Received on Thu Jul 05 2012 - 12:30:03 PDT
