cpptraj
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Amber-MD
Biomolecular simulation trajectory/data analysis.
E.g. sorted by a data set, random, etc.
This allows non-standard, user-defined distance metric in clustering analysis.
Less than 3 atoms means the covariance matrix will not be properly populated and cause the calculation to fail.
Add support for the following trajectory formats: - [x] TNG format - [ ] MMTF format http://mmtf.rcsb.org/ - [x] Desmond DTR format
Hello, For mixtures of two solvents ( A+B), A is 10% vol:vol conc and B is TIP3P water. purewater does not calculate the bulk free energy of the A co-solvent...
Hi, I am trying to find out which of the GIST columns are referenced to bulk water in order to compute the free energy. AMBER tutorial 25 suggests to compute...
Hi, while working on https://github.com/Amber-MD/pytraj/issues/1553, I've realized that `cpptraj` message is not very clear to me. ``` parm tz2.parm7 trajin tz2.nc rms myrms @CA radgyr myrms @CA nomax ``` Here...
I am using spam to calculate free energies for a mixed solvent MD simulation (protein is ABL kinase) My input file is as follows: parm /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4G_production.1.crd 1 50...
Dear Professor, I greatly appreciate if you would guide me to how I can calculate by ambertools the Interaction entropy for protein-protein binding like in (https://doi.org/10.1021/jacs.6b02682, DOI: 10.1021/acs.jcim.6b00734, http://dx.doi.org/10.1063/1.4978893]). Greeting,...
