Dear Amber Users!
I have a new issue with the cpptraj processing of an md trajectory of an
oligomeric system. The following script correctly removes the PBC effects
from the system, but from time to time the individual monomers jump over
the boundaries of the box:
parm parm.prmtop
trajin traj.netcdf 1 -1 1
trajout stripped.nc
strip :WAT,Na+,Cl-
#center :105,201
align .CA,C,O,N,H
autoimage
Alternatively I've tried using 'image centre known' instead of the
autoimage, but this hasn't solved the problem. Finally, I tried to centre
the system on the residues located in the centre of the system in the zone
between two protomers, but this didn't work as well. What additional tricks
could be useful to properly centre the system and avoid any artefacts
related to the PBC for such a case? mainly due to the parameterisation of
small compounds?
Many thanks in advance !
Enrico
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Received on Mon Mar 11 2024 - 07:00:02 PDT
