Dear Amber community:
I am trying to use ptraj to determine the distance as a function of time
from a water hydrogen to a serine hydroxyl in a pmemd simulation. The box
of waters contains more than 9999 WATs. The water I am interested in is
listed as B 533 in the ptraj output for the pdb file. My ptraj
input file to determine the distance as a function of time follows:
ptraj atpts_nowat_c0.5_init.top << eof
? trajin atpts_nowat_c0.5_md_500ps.crd 1 500 1
? distance file3 :231.OG :B533.H1 out og_h1.dat
? eof
The ptraj output ends as follows:
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin atpts_nowat_c0.5_md_500ps.crd 1 500 1
Checking coordinates: atpts_nowat_c0.5_md_500ps.crd
PTRAJ: distance file3 :231.OG :B533.H1 out og_h1.dat
Mask [:231.OG] represents 1 atoms
Mask [:B533.H1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Segmentation fault
I assume my problem is in the atom numbering for the WAT, but am not sure.
I would appreciate it if someone could point me in the right direction.
Thanks,
Ed Pate
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Received on Sun Apr 05 2009 - 01:11:25 PDT
