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Hello,
Could you add a tutorial of simulating GPCR proteins ? In the second step of preparing proteins, protprep.py can't recognize lipids (in my case POPC lipids prepared in Charmmgui) and therefor…
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I am generating and uploading data to CRIPT, but it appears that many data fields are ignored or not uploaded.
There is no error or warning thrown, which makes these very easy to miss.
I also don't …
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Hi, all!
Trying to use `XML` file with FF generated by **LigParGen** in **foyer**, and obviously receive an error message. Checking the fields of foyer `XML` file with OPLS-AA FF and the **LigParGe…
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When I run the opls function to perform PLS-DA analysis on the matrix, the Observation Diagnostics shows the OD and SD values. However, I am unable to get these values in the resulting object. Is ther…
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Hi there,
This is an example of GAFF forcefield file generation workflow from by dflow, details plz see https://github.com/cherushui/dflow_SMI2FF
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Hello,
I'm using the command called 'valence' which is one of the Tinker parameterization tools and I encountered the issue shown below:
```
###############################################…
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In the EMIM_scale0.8.itp file the CW-NA-CA-HA dihedral has coefficients V1 to V4: -2.7 5.65 0.355 0. See line 140 in the file. However, in the original paper "Development of OPLS-AA Force Fie…
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Hi,
we just merged an OpenMM pull request that disables the analytic dispersion correction in all LJ parameters coming from CHARMM force fields; https://github.com/openmm/openmm/pull/2359.
Amon…
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Hi
when issuing sudo python setup.py install command, I am facing following error that python.h is not found. Any help will be appreciated.
[sudo] password for jmondal:
running install
running bui…
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Hi!
I think there is a bug in LigGenPar 2.3 command line
I have installed it as advised, liked BOSS, etc.. when I do a test with smiles I get such output:
```
❯❯❯ LigParGen -s 'c1ccc(cc1)O' …