Dear Amber users,
we have been creating some pdb files using cpptraj and ptraj and we
have obtained an unexpected behaviour with cpptraj TER lines placement.
While ptraj introduces TER lines with the following format:
ATOM 9654 O WAT 606 34.075 42.652 49.927 0.00 0.00
ATOM 9655 H1 WAT 606 34.847 42.090 49.986 0.00 0.00
ATOM 9656 H2 WAT 606 34.145 43.065 49.067 0.00 0.00
TER 0 0
ATOM 9657 O WAT 607 56.460 89.789 45.998 0.00 0.00
ATOM 9658 H1 WAT 607 56.244 89.005 46.503 0.00 0.00
ATOM 9659 H2 WAT 607 56.470 89.492 45.088 0.00 0.00
cpptraj creates the following:
ATOM 9661 O WAT 606 34.075 42.652 49.927 0.00 0.00
ATOM 9662 H1 WAT 606 34.847 42.090 49.986 0.00 0.00
ATOM 9663 H2 WAT 606 34.145 43.065 49.067 0.00 0.00
TER 9664 WAT 606
ATOM 9665 O WAT 607 56.460 89.789 45.998 0.00 0.00
ATOM 9666 H1 WAT 607 56.244 89.005 46.503 0.00 0.00
ATOM 9667 H2 WAT 607 56.470 89.492 45.088 0.00 0.00
The problem is that the cpptraj format changes the atom index of the
atoms that follow a TER line and this may complicate further work using
this pdb file.
Is there anyway to keep using cpptraj while keeping the classic ptraj
TER line placement?
Best regards,
Iñigo.
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Received on Tue May 14 2013 - 07:00:02 PDT
