Dear,
I am using AMBER9 to equilibrate and run production dynamics on a protein.
Everything seems normal during the equilibration progress, but the PDB files
generated by "trajout" have some problems. I run the MD simulation with
"iwrap=1".
Form figure1, the picture of one of these PDB files, it is obvious to
find that the protein is at the edge of the box and some atoms stay outside
the water TIP3P box. It seems like there is a big ball-like thing in the
space.
So I try adding " center :1-150" and " image center familiar" to the
ptraj file to locate the solute molecule into box. Then I get the figure2
and 3, picture of new pdb file. In the new pdb, the water molecules are not
homogeneous. I want to get two or more box shown in pdb, but I don't know
how to get it.
Does someone have any suggestions to overcome the problems?
Looking forward to getting your help!
Thank you very much in advance!
Best Regards
--
Zhang Bingbing
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Received on Sun Sep 19 2010 - 19:00:05 PDT
