AMBER Archive (2009)

Subject: [AMBER] ptraj problem

From: Ed Pate (pate_at_math.wsu.edu)
Date: Fri Apr 03 2009 - 15:13:37 CDT


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_at_OG :B533_at_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_at_OG :B533_at_H1 out og_h1.dat
Mask [:231_at_OG] represents 1 atoms
Mask [:B533_at_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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