Dear Dan
I am very sorry. I get the following error massage
INPUT:
[trajin strip.md.nc]
Error: Number of atoms in NetCDF file strip.md.nc (5783) does not
match number in associated parmtop (43123)!
Error: Could not set up strip.md.nc for reading.
Error: trajin: Could not set up trajectory.
[rms :1-185 first]
[average chain1_1.pdb :1-185 pdb]
[rms :186-366 first]
[average chain2_1.pdb :186-366 pdb]
said
On Wed, Jan 7, 2015 at 9:47 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> First, you can combine those two strip commands into a single strip
> command. If you do indeed want a stripped topology file you need to
> add the 'outprefix' keyword like Dave mentioned before, e.g.:
>
> strip :WAT,Na+ outprefix strip
>
> Also, be aware that your average structures as the script is now will
> contain rotational and translational motion. You may want to create
> the average structures in a separate run from your stripped trajectory
> instead, with some rms-fitting to remove such motion from your
> averages, e.g.:
>
> parm 1blb_dimer.prmtop
> 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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> >>
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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)
>
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Received on Wed Jan 07 2015 - 12:30:02 PST
