Structural basis of actin monomer re-charging by cyclase-associated protein
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2018-01-31, 2018-01-31
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Pekka Lappalainen
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Description
1) table_of_simulations.pdf: table of simulations
2) toppar_HIC.str: methylhistidine (HIC) topologies and parameters
-prepared based on analogy
-to be used with top_all36_prot.rtf and par_all36_prot.prm
3) simulation_archive.tar.gz
The Contents:
1_ADP-Actin--CARP, 2_ADP-Actin--CAP1, 3_ATP-Actin--WH2, 4_ADP-Actin
All systems presented in the paper; see table_of_simulations.pdf
Each directory contains
000README gromacs_topologies gromacs_tpr_files index.ndx processed_trajectories prod.mdp systems_at_t=0
*** The rosetta models for WH2 domain and the proline-rich loop that connects it to the CARP domain can be found in 2_ADP-Actin--CAP1/rosetta_models
_Topologies:
toppar_c36_jul16:
The charmm force field version used to generate topologies before conversion to gromacs; see 000README in the systems directory
***toppar_c36_jul16/toppar_HIC.str: The topology and parameters for methylated histidine used in the simulations.
gromacs_topologies:
Contains all itp files (converted from psf file using PyTopol's psf2top utility) and parameters.
Note that relevant files can also be found in directories corresponding to each system ( 1_ADP-Actin--CARP 2_ADP-Actin--CAP1 3_ATP-Actin--WH2 4_ADP-Actin)