Hi All,
I have trouble when visualizing mdcrd trajectory in VMD 1.9.2. I have
searched the problem first but still cannot solve it.
I would like to generate one mdcrd file (only complex of protein-ligand,
increase time step to reduce size) from multiple mdcrd files from
simulation. What I have tried
parm com-sol.prmtop
trajin md1.mdcrd 1 500 50
trajin md2.mdcrd 1 500 50
...
autoimage
strip :WAT,Na+
trajout md-all.mdcrd
trajout md-all.pdb
md-all.pdb is normally visualized with VMD. But mdcrd file cannot. (Bonds
are distorted). I tried with com-sol.prmtop, md-all.mdcrd (Amber coordinate
with and without periodic box). I also make new prmtop without box
information and WAT, but still not working.
Could you please suggest me any idea to solve this problem.
Thanks in advance.
Trang
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Received on Tue May 10 2016 - 11:30:03 PDT
