[AMBER] pytraj native contacts

From: Rosellen, Martin <martin.rosellen.16.ucl.ac.uk>
Date: Wed, 23 Jan 2019 15:55:34 +0000


I want to write a programme in pytraj that returns the contacts with water of a given residue. In cpptraj it works fine and identifies 3 contacts:

nativecontacts :42 :WAT writecontacts 42_water_contacts.dat resout 42_water_contacts_resout.dat distance 2.0 out 42_water_contacts_out.dat includesolvent

I tried to do the same in pytraj but the behaviour of native_contacts is not clear to me:

pytraj.native_contacts(traj, mask=':42', mask2=":WAT", distance=2.0, include_solvent=True)

This gives me 927 contacts.

I want to further keep the data that gets written out to '42_water_contacts.dat' in the cpptraj command, in a variable python variable.

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Received on Wed Jan 23 2019 - 08:00:03 PST
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