AMBER Archive (2003)

Subject: AMBER: question about ptraj?

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Thu Jul 24 2003 - 11:18:20 CDT

Hi there:
   I try to do some trajectory analysis for the ligand which is bound to
a protein. I use ptraj to get the trajectory for the ligand from a MD
result. But I find a strange thing. This is the input file I use:
  
trajin md_nvt4_now_fit.crd
strip :970-976
strip :1-968
trajout test.crd
go

The ligand is residue #969. If I use this input file, I can get right
output (trajectory). But If I switch two 'strip' lines which means I
strip residue 1-968 first then 970-976. The program complains that it
can not find residue 970-976. Then the output file includes residue
970-976. Any clue? And if I want to keep some residues in the active
site. What should I do? How can I strip them correctly? 

-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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