Good afternoon,
I've modeled the interaction of a protein with its substrate and I would like to run a ASMD for a posterior PMF analysis or to grab enough distance frames for a umbrella sampling and PMF via WHAN calculation. Some researchers have done it perfectly before in other MD suites (DOI:10.1002/jcc.24502<
https://doi.org/10.1002/jcc.24502>, which is exactly what I need). However I don't know how to set the constrains correctly.
I need to move my ligand (residue 1 [atoms 1-303]) away from the protein (residues 2 - 460) active site. I found a tutorial on AMBER webpage entitled "Adaptive Steered Molecular Dynamics" however RST file is simply &rst iat=9,99, r2=13, r2a=17, rk2=7.2, &end, which is good for 2 atoms definitions.
How can I adapt this to something that means move atoms .1-303 and !(:1) away from 5 to 6 angstrons with a force constant of 30?
I've tried some other tutorials that defined a harmonic potential including parameters r1, r2, r3 and r4 and two force constants and group of atoms definitions, however I think this wouldn't move my ligand away from the protein, it would only keep it in a certain distance blocked by a potential, am I right?
My idea with all this is to calculate my binding affinity based on the lowest and highest PMF
Regards,
Frederico Henrique do Carmo Ferreira
NEQC-Núcleo de Estudos em Química Computacional
Universidade Federal de Juiz de Fora / Instituto de Ciências Exatas - Departamento de Química
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Received on Mon May 27 2024 - 14:30:02 PDT
