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Apr 30, 2024 · Biomolecular simulation trajectory/data analysis. Contribute to Amber-MD/cpptraj development by creating an account on GitHub.
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Oct 11, 2020 · Hi, while working on Amber-MD/pytraj#1553, I've realized that cpptraj message is not very clear to me. parm tz2.parm7 trajin tz2.nc rms ...
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Apr 13, 2021 · it was sorted out. It turns out the cmake build of Amber does not properly link the readline library for cpptraj; cpptraj uses readline for its
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... MD simulations of crystal structure (PDB ID: 1IG9) ... cpptraj. 650. 35.1. Introduction ... https://ambermd.org for an overview of the most important changes ...
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Sep 3, 2019 · level set to 1 or higher, e.g. ... > The version of cpptraj I am using is V17.00. ... > > First, could you say what version of cpptraj you are using ...
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I want to perform molecular dynamics of protein-ligand complex simulations by amber force field. but my ligand conatins 3 protonated amine. so can help me how ...
What does pytraj offer? How to get started; Contributors; Citations; Contact. pytraj is a Python front-end package of the popular cpptraj program.
Oct 3, 2018 · Figure 2 shows an example of the performance benefit from across-trajectory parallelization for calculating the coordinate RMSD of 1293 atoms ...
[INFO ] No ligand structure file was defined. Using ST approach... [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal ligand: ...
Aug 12, 2023 · > My problem is that when I process the trajectory file with cpptraj and > ... > Warning: 1 molecules have non-contiguous segments of atoms. > 1 2 ...
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