Hello, I got this error when I was trying to minimize a structure. please tell me what went wrong. Executing testchim.py...Opening test1_chimera.mol2...1 model opened Traceback (most recent call last): File "/data/pgm/chimera/chimera_1.2422/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "testchim.py", line 10, in ? rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "CHIMERA/share/chimera/__init__.py", line 1912, in runCommand File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand File "CHIMERA/share/MMMD/ChimeraExtension.py", line 29, in cmdMMMD File "CHIMERA/share/Midas/midas_text.py", line 281, in doExtensionFunc File "CHIMERA/share/Midas/midas_text.py", line 1885, in _getRealKw MidasError: Keyword 'nsteps' doesn't match any known keywords Error while processing testchim.py: MidasError: Keyword 'nsteps' doesn't match any known keywords (see reply log for Python traceback info) This is my program. I tried to execute it from command line using chimera --nogui testchim.py import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/data2/di/database_build/outputs/outputs_mol2_sdf") fn = "test1_chimera.mol2" rc("open " + fn) rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format mol2 0 min/" + fn) rc("close all") rc("stop now")
Hi Divya, In the 1.2422 release that you are using there is no "nsteps" keyword. In that version it was called "steps". The documentation that corresponds to your version is bundled with you version (use your Chimera's Help menu or type "help command-name" in its command line). Documentation on the web corresponds (depending on where you look) either to the current production release [1.5.3] or the current daily build [1.6]. I would highly recommend that you upgrade to a current version of Chimera since many improvements have been made to the minimization code (and everything else really) since the 1.2422 build (which is more than 4 years old after all). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 1, 2011, at 11:09 AM, divya neelagiri wrote:
Hello,
I got this error when I was trying to minimize a structure. please tell me what went wrong.
Executing testchim.py...Opening test1_chimera.mol2...1 model opened
Traceback (most recent call last): File "/data/pgm/chimera/chimera_1.2422/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "testchim.py", line 10, in ? rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "CHIMERA/share/chimera/__init__.py", line 1912, in runCommand File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand File "CHIMERA/share/MMMD/ChimeraExtension.py", line 29, in cmdMMMD File "CHIMERA/share/Midas/midas_text.py", line 281, in doExtensionFunc File "CHIMERA/share/Midas/midas_text.py", line 1885, in _getRealKw MidasError: Keyword 'nsteps' doesn't match any known keywords Error while processing testchim.py: MidasError: Keyword 'nsteps' doesn't match any known keywords (see reply log for Python traceback info)
This is my program. I tried to execute it from command line using chimera --nogui testchim.py
import os import chimera
from chimera import runCommand as rc from chimera import replyobj
os.chdir("/data2/di/database_build/outputs/outputs_mol2_sdf") fn = "test1_chimera.mol2" rc("open " + fn) rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format mol2 0 min/" + fn) rc("close all") rc("stop now")
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Hello, When I tried to minimize a molecule I got this error. Atom type Br is not supported ny MMTK. In the previous posts I read that we have to freeze that atom. Can you please tell me how do we do that from the command line. Thank you, Divya
Hi Divya, Actually freezing does not help, since that atom would still be included in energy calculations and exert forces on other atoms. I'm guessing it is an ion and not part of a molecule, because I believe GAFF/Antechamber can handle Br that is part of a small organic molecule. Your choices are to remove the Br ion from your structure, or to change it to Cl (chloride) either by text-editing the input file or doing it in Chimera, for example with commands: sel Br setattr a element 17 sel Although it won't solve this particular problem, for your future reference, the instructions for the "minimize" command including how to freeze are here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> ... or could be shown by entering the command: help minimize I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 20, 2011, at 1:37 PM, divya neelagiri wrote:
Hello, When I tried to minimize a molecule I got this error.
Atom type Br is not supported ny MMTK. In the previous posts I read that we have to freeze that atom. Can you please tell me how do we do that from the command line.
Thank you, Divya
Thank you very much!! On Tue, Dec 20, 2011 at 5:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Divya, Actually freezing does not help, since that atom would still be included in energy calculations and exert forces on other atoms. I'm guessing it is an ion and not part of a molecule, because I believe GAFF/Antechamber can handle Br that is part of a small organic molecule. Your choices are to remove the Br ion from your structure, or to change it to Cl (chloride) either by text-editing the input file or doing it in Chimera, for example with commands:
sel Br setattr a element 17 sel
Although it won't solve this particular problem, for your future reference, the instructions for the "minimize" command including how to freeze are here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
... or could be shown by entering the command: help minimize
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2011, at 1:37 PM, divya neelagiri wrote:
Hello, When I tried to minimize a molecule I got this error.
Atom type Br is not supported ny MMTK. In the previous posts I read that
we have to freeze that atom. Can you please tell me how do we do that from the command line.
Thank you, Divya
participants (3)
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divya neelagiri -
Elaine Meng -
Eric Pettersen