From: 辛志宏 <>
Date: Fri, 31 Jul 2020 11:46:21 +0800 (GMT+08:00)

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, “”:
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

Thank you for your help.

Zhihong xin
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Received on Thu Jul 30 2020 - 21:00:02 PDT
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