Dear Amber users,
Am trying to do SMD using the ncsu_smd code, trying to follow the LCOD
tutorial.
I have a trajectory of 200ns simulation Protein-ligand complex. planning to
pull ligand from different frames of trajectory and calculate the average
work done to remove the ligand.
I have few basic questions starting from placing the protein-ligand complex
and perform the calculation.
Generally in Gromacs protein will be placed on one corner of the
rectangular box and pull the ligand in the lengthiest direction with
explicit water. How can I do the same in amber?
How can I define the group of atoms? two sets as ligand to pull and protein
atoms to restraint? path?
and how to define the direction pulling in ncsu method.
I red the tutorial and still am not clear.
If I am wrong, Kindly suggest me which of the methods I can follow.
Thanks in advance
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Received on Sat Aug 25 2018 - 08:30:03 PDT
