Hi Colvin,
No this is nothing to worry about. I am not sure why ptraj is even looking
for that. The box dimensions should never be in the prmtop file (since they
change) and so I don't know why it would be looking for it. Certainly none
of AMBER's MD codes look for box dimension info in the prmtop - they only
look for if the prmtop represents a periodic system or not.
All the best
Ross
> -----Original Message-----
> From: colvin [mailto:colvin4367.gmail.com]
> Sent: Thursday, May 17, 2012 8:39 PM
> To: AMBER Mailing List
> Subject: [AMBER] prmtop generated from chamber
>
> Dear all,
>
> After running MD simulations using the prmtop file generated from
> chamber, i used ptraj to process the trajectories and run rmsd.
>
> In the ptraj output, it stated that "PRMTOP does not contain %FLAG
> BOX_DIMENSIONS there were errors upon reading parm file". I then check
> the prmtop file generated using chamber and it really doesn't has box
> info. The box dimension and angle are only found in my inpcrd file.
> Despite this errors, i am still able to process my trajectories and
> get the result for rmsd calculation. Is this important to concern
> about?
>
> Pls advise.
>
> Thanks and regards,
> Colvin
>
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Received on Fri May 18 2012 - 10:30:05 PDT
