cpptraj
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Amber-MD
Biomolecular simulation trajectory/data analysis.
Currently K-Means initialization is more or less random, followed by picking points distant from each other. There should be an option to use points of high density for initialization (similar...
Hi, I am tracking the tryptophan dihedral (chi1,chi2) of 2 different systems with ``` parm prod1/structure.psf trajin prod$1/output.xtc strip :SOD,CLA,TIP3 autoimage rms first @CA dihedral :X@N :X@CA :X@CB :X@CG out...
Reported on the Amber mailing list on 3-15-2024 by user Hirosuke Hotta: ``` Dear cpptraj developers, Regarding cpptraj error with test "Test_SPAM". We found Test_SPAM (there are 2 tests in...
In collaboration with @ramirandaq @lexin-chen, expand the cluster analysis capabilities of cpptraj by adding clustering via extended similarity metrics (and more). Some background reading: https://link.springer.com/article/10.1186/s13321-021-00505-3 https://link.springer.com/article/10.1007/s10822-022-00444-7
Dear all, I have converted my topology file with added PDB information (like chain ID and renumbering PDB) using "parmed". However, the previously mentioned information still missing in output file...
Hello, I want to get the Distribution of the tetrahedral order parameter Q for TIP4P/2005 water model. I have run NPT and have eq_npt.nc trajactory file and wtr_1.prmtop as topology...
i have been trying to get Local structure index (LSI) of water TIP4P/EW by running NPT through cpptraj by using following commands. parm tip4p/ew.parm7 trajin eq_npt.nc solvent :WAT hbond watcoord...
Maybe cpptraj can already do this... ? I would like to have NAStruct local axis information for both bases and base pairs made available alongside the other pairing and step...
The GIST output and Eww output are currently ASCII, which can be cumbersome for large numbers of voxels. Would be nice to have the option to write to e.g. NetCDF....
Hi I am trying with `bash configure -shared -macAccelerate -noarpack -nosanderlib clang` Then I picked `n` for the answer but getting error: ``` Checking NetCDF4/HDF5: Checking HDF5: Checking for bundled...
