Hello,
I want to use AMBER to run a simulation of a membrane protein, small molecule and POPC bilayer membrane complex system, and the complex parameter files .inpcrd and .prmtop have been generated by tleap.
But I do not know how to optimize and balance the system. I searched some posts on the Internet and summed up the following optimization and balancing steps:
(1) Energy minimization of water and ions;
(2) Energy minimization of protein, small molecule and POPC;
(3) Heating system to 310K;
(4) Balancing water and ions using NVT ensemble;
(5) Balancing POPC using NPT ensemble;
(6) Balance protein and small molecule using NPT ensemble;
(7) Conventional molecular dynamics simulation under the NPT ensemble.
Whether this optimization and balancing process suitable for membrane protein, small molecules and POPC system? If not, which step needs to be improved?
In addition, if a residue of small molecule in .prmtop file is named SW2, how can I use the 'restraintmask' instruction in the .in file to restrict the small molecule?
Thank you!
Best wishes!
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