For the restraints list, you can set iat to -1 and then give a mask using
igr, it will use the COM of that group.
Info is in the manual, or see this post in the archives
http://archive.ambermd.org/201708/0356.html
On Mon, May 27, 2024, 5:22 PM Frederico Henrique Ferreira via AMBER <
amber.ambermd.org> wrote:
> 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 - 16:30:02 PDT
