Dear Jason Swails and Bill Ross
before, I visualized my generated .prmtop and .inpcrd files by VMD.
but this time, at first, as Bill said, I used
$AMBERHOME/exe/ambpdb -p com.prmtop < com.inpcrd > com.pdb.
when I visualize generated com.pdb file by VMD, attached figure is created.
in that water, Na+, DNA are good and normal but protein is unusual
(1- there is no connection between residues. 2- hydrogen atoms are as dot
and didn't connect to other atoms. 3- there are undesirable bonds between
atoms)
I specified undesirable atoms by white squares.
for ease, I deleted waters and Na+. protein and DNA are located on the right
and left of figure, respectively.
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Received on Sun Dec 12 2010 - 10:00:06 PST
