AMBER Archive (2004)

Subject: Re: AMBER: reference with ptraj

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hello

you must specify the atom or residu in the command line, the manul of Ptraj
should help you
good luck
ju_at_n

John a écrit :

> Hello,
>
> I want to calculate the rmsd against a reference file. Here is the input
> file:
>
> trajin annealing.traj 175 200
> average average.pdb pdb
> rms referernce out allatoms
>
> According to the output file the crd and pdb files are being read but I get
> the following message:
>
> ACTIONS
> 1> RMS to first frame using no mass weighting
> Dumping RMSd vs. time (with time interval 1.00) to a file named
> allatoms
> Atom selection follows [No atoms are selected]
>
> No atoms are selected and I get the rmsd against the first frame. Any idea
> what is wrong with the input file?
>
> Many thanks for the help.
>
> John
>
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