Greetings everyone!
I want to perform steered molecular dynamics (SMD) simulation using AMBER20
and need to define the center of mass (COM) of two domains of a protein in
the DISANG file.
Could anyone kindly share a sample DISANG file or example input that
demonstrates how to define COM of two domains in order to change
the distance between them?
For reference, I’ve included a standard DISANG file format for a distance
restraint between two atoms:
# Change distance between atoms 485 and 134 from 15 A to 20.0 A
&rst iat=485,134, r2=15., rk2 = 5000., r2a=20.0, /
Any guidance, suggestions, or example files would be greatly appreciated.
Thanks and regards,
Gourav Das
Research Scholar
IIT Kharagpur
India
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Received on Sat Sep 20 2025 - 00:00:02 PDT
