Residue selection for simulation/energy-minimization
Dear, I am trying to publish our structure and modeling done by CHIMERA. My questions are 1. What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand). 2. Any time scale for simulation? Here is my method description. Any suggestion, related citation, and help would be appreciated. “~. Residues within XX A of the ligand was selected for simulation. The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).” Thanks, In-Kwon In-Kwon Kim, Ph.D. Assistant Professor Department of Chemistry University of Cincinnati
Dear In-Kwon, There is no default distance for selecting residues. The “minimize structure” dialog has a choice to “fix” (freeze) some atoms, but by default, no atoms are frozen: the whole structure can move. If somebody selected some atoms to hold “fixed” that are farther than some distance from the ligand, they would have to enter the distance. I have no idea if that was done or what value was entered. Maybe only the residues close to the ligand were displayed. However, this has no relationship on what can move. Minimization is not a simulation, it is only minimization. Although there are “steps” they are not time steps, so there is no time scale. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 19, 2018, at 2:33 AM, Kim, In-Kwon (kimiw) <kimiw@ucmail.uc.edu> wrote:
Dear, I am trying to publish our structure and modeling done by CHIMERA. My questions are • What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand). • Any time scale for simulation?
Here is my method description. Any suggestion, related citation, and help would be appreciated.
“~. Residues within XX A of the ligand was selected for simulation. The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).”
Thanks,
In-Kwon
In-Kwon Kim, Ph.D. Assistant Professor Department of Chemistry University of Cincinnati _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, Thank you very much for your comments. It helps a lot. Best, In-kwon In-Kwon Kim, Ph.D. Assistant Professor Department of Chemistry University of Cincinnati On 4/19/18, 12:28 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Dear In-Kwon, There is no default distance for selecting residues. The “minimize structure” dialog has a choice to “fix” (freeze) some atoms, but by default, no atoms are frozen: the whole structure can move. If somebody selected some atoms to hold “fixed” that are farther than some distance from the ligand, they would have to enter the distance. I have no idea if that was done or what value was entered. Maybe only the residues close to the ligand were displayed. However, this has no relationship on what can move. Minimization is not a simulation, it is only minimization. Although there are “steps” they are not time steps, so there is no time scale. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 19, 2018, at 2:33 AM, Kim, In-Kwon (kimiw) <kimiw@ucmail.uc.edu> wrote: > > Dear, > I am trying to publish our structure and modeling done by CHIMERA. > My questions are > • What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand). > • Any time scale for simulation? > > Here is my method description. Any suggestion, related citation, and help would be appreciated. > > “~. Residues within XX A of the ligand was selected for simulation. The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).” > > Thanks, > > In-Kwon > > In-Kwon Kim, Ph.D. > Assistant Professor > Department of Chemistry > University of Cincinnati > _______________________________________________ > Chimera-users mailing list: Chimera-users@cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Kim, In-Kwon (kimiw)