Dear Dan
My full script is
parm 1blb_dimer.prmtop
trajin 1blb_dimer-prod-1.mdcrd 1 50 1
-
-
-
strip :WAT
strip :Na+
average chain1.pdb :1-185 pdb
average chain2.pdb :186-366 pdb
trajout strip.md.nc netcdf
Also I did not see the previous massage.
said
On Wed, Jan 7, 2015 at 9:33 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Wed, Jan 07, 2015, Ibrahim Said wrote:
>
> > I added the line parm protein.prmtop, but I did not get
> > strip.protein.prmtop.
>
> This sounds like progress, assuming that all the other error messages
> (relating to not being able to open the protein.prmtop file) are gone.
>
> > > > trajin 1blb_dimer-prod-1.mdcrd 1 50 1
> > > > -
> > > > -
> > > > -
> > > > trajin 1blb_dimer-prod-12.mdcrd 1 100 1
> > > > trajout strip.md.nc netcdf
>
> The above script doesn't have any "strip" commands in it. Are you actually
> expecting to strip atoms?
>
> If you want to get a stripped prmtop file (in addition to a stripped
> trajectory file), you need to have a "strip" line with the "outprefix"
> option.
> (And if you just want to combine several trajectory files into a single
> one,
> without stripping atoms, then there is no need to create a new prmtop
> file.)
>
> ...hope this helps...dac
>
>
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Received on Wed Jan 07 2015 - 12:00:03 PST
