System preparation with HTMD

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:

SAMSON.importFromFile('/path/to/1YRF.pdb')

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:

SAMSON.importFromFile('/path/to/1YRF-solvated.pdb')