I’m trying to generate a single pdb file from a trajectory by stripping all Na+ and all but one water molecule.
My input file is:
trajin equil_2ns.mdcrd 1 1
center :1-127 mass origin
image origin center familiar
strip_mask = :WAT,Na+,&!:127
trajout test.pdb pdb
The error message I get is:
PTRAJ: Processing input from file make.in
PTRAJ: trajin equil_2ns.mdcrd 1 1
Checking coordinates: equil_2ns.mdcrd
Rank: 0 Atoms: 13282 FrameSize: 322778 TitleSize: 81 NumBox: 3 Seekable 1
PTRAJ: center :1-127 mass origin
Mask [:1-127] represents 2024 atoms
PTRAJ: image origin center familiar
Mask [*] represents 13282 atoms
PTRAJ: strip_mask = :WAT,Na+,&!:127
ERROR in tokenize(): wrong syntax
‘;
I tried enclosing the expression of the strip_mask in “ “ and ‘ ‘ to no avail
Thanks in advance for any suggestions
Regards
George
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Received on Fri Mar 21 2014 - 08:00:02 PDT
