Dear all,
I have simulated an elongated protein in a cubic box (reason being the long
edges of the protein tilt during simulation and interact with its periodic
image thus resulting in bad energy values when I had used a cuboid /
triclinic box ). Now the substrate inside the protein often moves out in
certain frames during the simulation. Upon visualization, I saw that the
substrate molecule that moved out, is now becoming a part of its periodic
image.
I tried to image using ptraj with following script, but the substrate is
not imaged back to the protein.
*trajin md20.dcdcenter :1-476 originimage center origin familiarcenter
:1-486 mass originimage origin center familiarcenter :1-488 mass
originimage origin center familiarcenter :1-504 mass originimage origin
center familiartrajout centered_200.dcd charmm nobox*
*Note- *
1to 476: protein residues
1-486: including one substrate
1-488: including second substrate
1-504: including protein,substrates and the inhibitor
When I do a calculation, especially like binding energy, will the substrate
be rightly considered in the calculation?
How can I rectify this, if it is just an imaging problem?
Kindly give your valuable suggestions in this regard.
thank you in advance.
Revathi.S
M.S. Research Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute Of Technology, Madras
India
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Received on Mon Jun 09 2014 - 04:30:02 PDT
