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It's all just set with the defaults, because when the system.xml is deserialized, it does not interact with the config system.
cc @mpharrigan
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So often when we add a feature to the Python App, we want to compare two system objects to check for equality of force field parameters. For example, in my GAFF work I want to evaluate whether my XML…
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Hi Robert,
Running the OpenMM command line app with the config file produced the following error. I attached the inputs. Over the next few days, it seems we might want to iron out the config file p…
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I was trying to use ConvertDataToHDF.py and kept getting this error:
IndexError: index (988) out of range (0
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Thankes for your reply.
Recently, i'm doing my protein by MSMBuilder 2.5. In my protein, there are 5567 atoms, my protein is a protein-protein compound.
When i run 'GetRandomConfs.py -c 1 -f pdb' co…
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Hi,
Now, i have a problem about ConvertDataToHDF.py command.The following is my fault durning running:
## [root@localhost Chimera4-1]# ConvertDataToHDF.py -t 3 -s c4-18-3.pdb -i XTC
MSMBuilder versio…
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Hi
When i run :Cluster.py dihedral hybrid -k 100, it appears the fllowing fault :
## [root@localhost hil-21-3a3]# Cluster.py dihedral hybrid -k 100
MSMBuilder version 2.6.0.dev-Unknown
## See file A…
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First,I provide my info about my project:
1, it is a protein
2, there are 134 amino acids and 2184 atoms in my PDB file
my problem is the following:
```
[root@localhost hil-21-2p2-2-MSM]# SaveStruct…
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dear friend:
When I use NMWiz 1.0 ,prody 1.1 and python 2.7, I come across the error.
Traceback (most recent call last):
File "C:/Python27/Lib/site-packages/prody/dynamics/anm.py", line 35, in
…
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Move module usage reference to module documentation so that users can get instant help, as in the case of atom selections.
> > > help(atomic) # should highlight important features of atomic classes
>…