Dear all:
I have done a molecular dynamics. But I encounter a problem when I see the structure. The attached file am_cro_md.rst is my last structure of molecular dynamics trajectory, and md.in and am_cro.prmtop are the control and top files. I convert the structure to the pdb file using cpptraj:
trajin am_cro_md.rst
trajout am_cro_md1.pdb
This structure seems no periodic. So I use the image tool:
trajin am_cro_md.rst
image center
trajout am_cro_md2.pdb
This two structures are different. The metal ion coordinates with two NO3- for first structure, but with three NO3- for second structure.They are so strange. I want to choose some solvent to do QM/MM optimization. So I do not know choose which structure. Is there something wrong? Can anyone give me a help?
With my best regards,
Junbo
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Received on Wed May 03 2017 - 20:30:02 PDT
