when I run minimization step, I look at the structure, with help VMD to
visualize complex_solvated.pdb and complex_solvated_min2.pdb
( ambpdb -p complex_solvated.prmtop < complex_solvated.inpcrd >
complex_solvated.pdb
ambpdb -p complex_solvated.prmtop < min2.rst > complex_solvated_min2.pdb )
I compared the starting structure and the minimized structure. I can see the
the structure has changed slightly, and I think that there are no major
problem.
If I don't have good minimized structure, What do I do? How do I understand
it?
As I said before, I calculated MD (heating) with ntwx=1 ntpr=1 ntslim=100 ,I
saw heat.mdcrd and complex_solvated.prmtop files by chimera software!
When I use ptraj comment, I can't show RMSD of diagram because I have zero
for all.
I use this script (rmsd.in) :
"trajin heat.mdcrd
reference min2.rst
rms reference out RMSD.rms "
and then I run;
ptraj complex_solvated.prmtop < rmsd.in
please give your valuable comment.
thanks in advance.
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Received on Mon Feb 23 2015 - 04:30:03 PST
