AMBER Archive (2008)

Subject: AMBER: wrapping w/ ptraj

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Fri Aug 29 2008 - 16:57:52 CDT

Hi,

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 

-- 

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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