Hi: I have noticed that scripts can start with: import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector. Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation? Any suggestions would be appreciated. Cheers, Forbes
Chimera's "Structure Editing -> Minimize Structure" tool (or the "minimize" command) may be used to do this. The tool reports the initial energy of the system in the Reply Log. If you give zero as the number of steps for both steepest descent and conjugate gradient minimization, then Chimera should return immediately. Conrad On 4/13/12 7:09 AM, Forbes J. Burkowski wrote:
Hi:
I have noticed that scripts can start with:
import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField
We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector.
Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation?
Any suggestions would be appreciated.
Cheers, Forbes _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Forbes, The minimization tool reports the total energy, not any breakdown into components (electrostatic, VDW, strain) or interactions between sets of atoms. However, the "minimize" command has a "fragment" option for ignoring all but the specified residues, so you could at least limit what is considered the total system. That also makes the calculation faster, although single-point energy calculation (0 steps minimization) should already be pretty fast. Best, Elaine Example (and see also "nogui true"): minimize spec :13.a,17.a fragment true cgsteps 0 nsteps 0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> On Apr 13, 2012, at 10:38 AM, Conrad Huang wrote:
Chimera's "Structure Editing -> Minimize Structure" tool (or the "minimize" command) may be used to do this. The tool reports the initial energy of the system in the Reply Log. If you give zero as the number of steps for both steepest descent and conjugate gradient minimization, then Chimera should return immediately.
Conrad
On 4/13/12 7:09 AM, Forbes J. Burkowski wrote:
Hi:
I have noticed that scripts can start with:
import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField
We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector.
Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation?
Any suggestions would be appreciated.
Cheers, Forbes _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi: Thanks for the response. The code that you suggested seems to work. I am getting the initial energy reported in the Python Shell along with other lines that are reporting on the activities of the command. Since I am embedding this command in a runCommand statement, I would like to get the initial energy value put into a variable within the Python script instead of the Python Shell window. Is there any way to accomplish this? Cheers, Forbes On Fri, 13 Apr 2012, Elaine Meng wrote:
Hi Forbes, The minimization tool reports the total energy, not any breakdown into components (electrostatic, VDW, strain) or interactions between sets of atoms. However, the "minimize" command has a "fragment" option for ignoring all but the specified residues, so you could at least limit what is considered the total system. That also makes the calculation faster, although single-point energy calculation (0 steps minimization) should already be pretty fast. Best, Elaine
Example (and see also "nogui true"):
minimize spec :13.a,17.a fragment true cgsteps 0 nsteps 0
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
On Apr 13, 2012, at 10:38 AM, Conrad Huang wrote:
Chimera's "Structure Editing -> Minimize Structure" tool (or the "minimize" command) may be used to do this. The tool reports the initial energy of the system in the Reply Log. If you give zero as the number of steps for both steepest descent and conjugate gradient minimization, then Chimera should return immediately.
Conrad
On 4/13/12 7:09 AM, Forbes J. Burkowski wrote:
Hi:
I have noticed that scripts can start with:
import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField
We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector.
Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation?
Any suggestions would be appreciated.
Cheers, Forbes _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Forbes, If you want to get the minimized energy within your Python script then you need to run the minimization using a Python function call rather than a Chimera text command. To figure out how to do that I look at the Python code that is called by the Chimera text command in your Chimera distribution chimera/share/MMMD/cmdline.py or also available online http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/MMMD/cmdline.py The minimize() Python function is called using the text command arguments. I see it basically does from MMMD import base minimizer = base.Minimizer(molecules, nsteps, stepsize, cgsteps, cgstepsize, interval, fixedAtoms, memorize, nogui, addhyd, lambda m: m.run(), exclres, cache, prep) Looking at base.py in the same directory and tracking back from where "Initial energy..." is printed in file MMTKinter.py I see the energy is obtained using minimizer._mi.universe.energy() I have not tested this out but perhaps it will move you in the direction you want to go. Tom
Hi:
Thanks for the response. The code that you suggested seems to work. I am getting the initial energy reported in the Python Shell along with other lines that are reporting on the activities of the command.
Since I am embedding this command in a runCommand statement, I would like to get the initial energy value put into a variable within the Python script instead of the Python Shell window. Is there any way to accomplish this?
Cheers, Forbes
On Fri, 13 Apr 2012, Elaine Meng wrote:
Hi Forbes, The minimization tool reports the total energy, not any breakdown into components (electrostatic, VDW, strain) or interactions between sets of atoms. However, the "minimize" command has a "fragment" option for ignoring all but the specified residues, so you could at least limit what is considered the total system. That also makes the calculation faster, although single-point energy calculation (0 steps minimization) should already be pretty fast. Best, Elaine
Example (and see also "nogui true"):
minimize spec :13.a,17.a fragment true cgsteps 0 nsteps 0
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
On Apr 13, 2012, at 10:38 AM, Conrad Huang wrote:
Chimera's "Structure Editing -> Minimize Structure" tool (or the "minimize" command) may be used to do this. The tool reports the initial energy of the system in the Reply Log. If you give zero as the number of steps for both steepest descent and conjugate gradient minimization, then Chimera should return immediately.
Conrad
On 4/13/12 7:09 AM, Forbes J. Burkowski wrote:
Hi:
I have noticed that scripts can start with:
import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField
We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector.
Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation?
Any suggestions would be appreciated.
Cheers, Forbes _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Conrad Huang -
Elaine Meng -
Forbes J. Burkowski -
Tom Goddard