AMBER Archive (2000)

Subject: Re: DOUBT IN AMBER5 PTRAJ DOCUMENTATION (fwd)

From: A.Madhumalar (malar_at_mbu.iisc.ernet.in)
Date: Wed May 24 2000 - 05:53:32 CDT

---------- Forwarded message ----------
Date: Tue, 23 May 2000 10:07:21 -0700 (PDT)
From: jim caldwell <caldwell_at_heimdal.compchem.ucsf.edu>
To: A.Madhumalar <malar_at_mbu.iisc.ernet.in>
Subject: Re: DOUBT IN AMBER5 PTRAJ DOCUMENTATION

Please post this to amber_at_cgl.ucsf.edu

On Tue, 23 May 2000, A.Madhumalar wrote:

> 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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