AMBER Archive (2000)

Subject: Re: DOUBT IN PTRAJ DOCUMENTATION

From: A.Madhumalar (malar_at_mbu.iisc.ernet.in)
Date: Wed May 24 2000 - 02:05:12 CDT

 Dear sir,
        I am using AMBER5 for molecular dynamics of DNA.I wanted to use
 grid option in ptraj documentation for hydration analysis,before that i
 was trying to do rmsfit with rdparm.my input is like this
 
 ptraj parmtop << EOF
 trajin mdcrd199 1 10
 trajin mdcrd198 1 10
 trajin restrt199
 traj.out fixed.traj
 rms previous
 image
 center origin
 go
 EOF
         it is not at all reading the input file.And also in rdparm if
 i give mainmenu option as analyze it is saying as not found in tokenlist.
 could you please suggest me some ways to utilise these analysis
 programs.Thanks in advance.

 sincerely,
 madhu
 
 

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