Thanks!
On Sun, Nov 26, 2017 at 11:34 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Use energy post-processing (imin=5) with energy minimization options
> set as you want them in sander. See manual for more details.
>
> -Dan
>
> On Sat, Nov 25, 2017 at 10:24 PM, Abdul-Rashid III Sampaco
> <absampaco.up.edu.ph> wrote:
> > Hello,
> >
> > I have a 1000ns netcdf trajectory file (i wrote a new structure every 1ps
> > so the file contains 1 million structures). It is basically a
> > conformational search of a small peptide. Is it possible to perform
> energy
> > minimization on all the structures in the file without having to rewrite
> > each one to a new file and iterating over them with a separate sander
> > command? Thanks.
> >
> > I have already tried using the nc file as an input to sander like as
> > follows:
> >
> > sander -O -i min.in -o min.out -c md.nc -r min_md.rst -p md.parm7
> >
> > It turns out sander only accepts crd and rst7 files.
> >
> >
> > Rashid
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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>
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Received on Sat Nov 25 2017 - 20:00:04 PST
