Dear Dan
This is the first error I have faced. cpptraj can not write this
strip.1blb_dimer.prmtop.
said
On Wed, Jan 7, 2015 at 10:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Sorry, you need to use the stripped topology of course:
>
> > parm 1blb_dimer.prmtop
>
> should instead be
>
> parm strip.1blb_dimer.prmtop
>
> which should have been generated in the previous step.
>
> -Dan
>
> > trajin strip.md.nc
> > rms :1-185 first
> > average chain1.pdb :1-185 pdb
> > rms :186-366 first
> > average chain2.pdb :186-366 pdb
> >
> > -Dan
> >
> > On Wed, Jan 7, 2015 at 12:39 PM, Ibrahim Said <saidibrahim569.gmail.com>
> wrote:
> >> 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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> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 07 2015 - 13:00:02 PST
