System preparation with HTMD
HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems.
HTMD (by Acellera) can be integrated into, for example, protein preparation pipeline in SAMSON.
HTMD can be installed through Anaconda:
conda install -c acellera htmd
Let us import a molecule into SAMSON:
Now, you may use any instrument provided by SAMSON to interactively modify the system, e.g., the Twister App.
The easiest way to use HTMD inside SAMSON is to export the modified molecule into a pdb-file or another format supported both by SAMSON and HTMD.
indexer = SAMSON.getNodes('n.t sm') # get an indexer of structural models SAMSON.exportToFile(indexer, '/path/to/1YRF-twisted.pdb') # export data contained in the indexer into a file
Let us now use HTMD from within SAMSON for further preparation of the system:
from htmd.ui import * mol = Molecule('/path/to/1YRF-twisted.pdb') mol_op = proteinPrepare(mol) mol_seg = autoSegment(mol_op) mol_solv = solvate(mol_seg, pad=10) mol_solv.write('/path/to/1YRF-solvated.pdb')
Now you can import the prepared molecule back to SAMSON: