AMBER: wrapping w/ ptraj

From: Arturas Ziemys <>
Date: Fri, 29 Aug 2008 16:57:52 -0500


I got unwrapped trajectory from Amber 9 (protein+water). I want to use
ptraj to wrap it and save it for later use in wrapped (rectangular)
state. I use my ptraj script like this:
  trajin ../prod1.mdcrd 1 20
  center origin :1-217
  image origin center familiar
  trajout prod1_wrapped.mdcrd

However, I get something irrelevant: my protein structure is distorted
(all atoms). How to get that trajectory right ?


Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929  
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Received on Sun Aug 31 2008 - 06:08:03 PDT
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