Re: [AMBER] pbsa calculation

From: Ray Luo <rluo.uci.edu> Date: Tue, 30 Jul 2019 11:49:21 +0800

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Tue, Jul 30, 2019 at 8:39 AM Lod King <lodking407.gmail.com> wrote:
>
> Hi Amber
>
> I referred to the AMBER 18 manual to calculate the single point E using the
> following: (section 6.2.1)
>
> *$pbsa [-O] -i mdin -o mdout [-p prmtop -c inpcrd]/[-pqr pqr]*
>
> I wonder is there a flag to specify a traj, instead of using the initial
> frame, because i got the following error message:
>
> *$pbsa -O -i mdin.in <http://mdin.in> -o mdout.out -p new.prmtop -y
> rmsd_ca_1.dcd *
>
>
>
> *     ERROR: Unknown argument: -y
>                                         usage: pbsa  [-O] -i mdin -o mdout
> [-p prmtop -c inpcrd/-pqr pqr]Consult the manual for proper file usages.*
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