Thank you David.
I refer a method from a reference " The reactant state was taken from the previously minimized structure, upon deletion of all water molecules beyond a shell of 5A around the enzyme-substrate complex",
so, I saved the last frame as QM/MM input file, and then recreat inpcrd and prmtop file due to the quantity of total molecular changed.
I saved the rst file by cpptraj from the equil mdcrd file (the box in the end of the rst file) according your suggestion, and then run QM/MM, but a new error occured, I do not know how to fix it,
............
Small interatomic distances encountered:
54 49 4.54D-01
Atoms too close.
In addtion,I got more than 500 rst file when I saved the rst file by the following script, how to only save the rst file of the last frame from the mdcrd file?
Create an input file, “ptraj.in”:
—————————————————————————————————————
trajin DLFae4-MFA_equil.mdcrd
image center
trajout DLFae4-MFA_equil_reimaged.mdcrd
trajout DLFae4-MFA_equil_reimaged.rst (or 499.rst)
__________________________________
cpptraj DLFae4-MFA-complex-wat.prmtop ptraj.in
Thank you for your help.
Zhihong xin
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Received on Thu Jul 30 2020 - 21:00:02 PDT
