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

From: Mark Abraham <>
Date: Fri, 21 Jan 2011 14:08:57 +1100

On 21/01/2011 1:47 PM, Daniel Roe wrote:
> Hi,
> 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.

OK. Shouldn't -A on nonexistent files warn the user that this is not a
desirable combination?

Your fix worked, thanks!


AMBER mailing list
Received on Thu Jan 20 2011 - 19:30:03 PST
Custom Search