cpptraj
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Amber-MD
Biomolecular simulation trajectory/data analysis.
Hi Dan, Just wondering if we can do a per frame print out of pdb file rather than using trajout to print a gigantic file containing 1000+frames. Is this possible...
Hi, I'm using GIST to measure energetics of water displacement upon ligand binding to a protein cavity. I've been following this [tutorial from ambermd.org](https://ambermd.org/tutorials/advanced/tutorial25/section4.htm). It is my understanding that to...
- [ ] `nointrares` keyword? - [x] bridging time series? - [x] Ignore UA - V -UA bridges with nointramol hbond - [x] allow bridges within one residue - [x]...
Related to #999 . - [ ] NetCDF4/HDF5 writes should work in parallel. - [ ] Cmake should know how to build with NetCDF4/HDF5. - [ ] The `-libstatic` configure...
Hi, I've been running MD simulations using OpenMM and want to carry out water analysis using GIST. While I haven't restrained the protein using strong position restraints, as suggested by...
Hi Dan I have been doing some druggability simulations on AMBER22 and I am interested to calculate the volume of a pocket (could be transient) defined by residue name list...
Hi, Should be the message clearer? something like "checking netcdf -> does not exist -> offer to install?" ``` configure command: bash configure -shared -macAccelerate -noarpack -nosanderlib clang arpack disabled....
GIST in CPPTRAJ now has a lot of functionality thanks to all the work being done from @fwaibl @tkurtzman @EricChen521 @jokr91 @gosldorf and others. I think that developing some tutorials...
Amber20, please add a "range360" keyword to phipsi analysis. Thank you.
Specifically `vector corrplane` has two equally correct solutions, but when calculating angles from `corrplane` you typically want the acute one.