Re: [AMBER] problem with GB REMD trajectories and ptraj

From: Daniel Roe <>
Date: Thu, 20 Jan 2011 21:47:18 -0500


I think this is the issue:

On Thu, Jan 20, 2011 at 9:05 PM, Mark Abraham <> wrote:
> with group file
> -O -A -rem 1 -i -p ../../../leap/ -c
> ../equil/equil0.rst -o sim0.out -x sim.mdcrd.000 -r sim0.rst -inf sim0.inf

You're specifying the '-A' (append) flag for a brand new simulation,
so your trajectories don't have a title line which is the standard for
Amber formatted trajectories (and which ptraj expects). If you add a
fake title line to the top of each of your trajectories everything
should be fine.


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Received on Thu Jan 20 2011 - 19:00:04 PST
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