Hi,
You could use the 'mask' command or you could use a combination of
'strip'/'unstrip' and 'outtraj' (which is what I usually do). E.g.
cpptraj <<EOF
parm *.prmtop
trajin nvt10.ns.rst7
strip "!((:1 <: 5) & ! :1)"
outtraj host.pdb
unstrip
strip "!(:1)"
outtraj guest.pdb
run
EOF
Note that I'm negating your original masks, which effectively turns
'strip' into "keep".
Hope this helps,
-Dan
On Wed, Aug 7, 2019 at 9:43 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Hang on one second
>
> Since there was a flag allowing reading the .nrst file, maybe I don’t need to convert and pass to ambmask for my purpose as the “mask” available in cpptraj should work just fine.
>
> What I am doing right now is the following:
>
> $ ambmask -p *.prmtop -c nvt10ns.rst7 -prnlev 0 -out pdb -find '(:1 <: 5) & ! :1' > host.pdb
> $ ambmask -p *.prmtop -c nvt10ns.rst7 -prnlev 0 -out pdb -find ':1' > guest.pdb
>
> This works fine, printing every residue within 5 angstroms from 1 excluding 1 itself to one “host” file and just residue 1 to another “guest” file which can then be used to set up docking runs.
>
> Can I not just use the mask function in cpptraj (which seems identical) to accomplish the same thing? Reading in the .nrst files as described and then creating the same output and then skipping the in-between step of file conversion?
>
> Best regards
> // Gustaf
>
>
> > On 7 Aug 2019, at 14:06, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > cpptraj -p topology.parm7 -y restart.nrst -x restart.rst7
> >
> > -Dan
> >
> > On Wed, Aug 7, 2019 at 7:41 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> >>
> >> As the title states, a lazy search for a shortcut so as not having to figure it out by myself.
> >>
> >> What would be the "most scriptable”, non-GUI and fast way to convert from NCRST to old RST(7) format using anything available in the amber/ambertools package?
> >>
> >> I need to convert a number of new binary format to the old ASCII format to process with another program.
> >>
> >> Best regards
> >> // Gustaf
> >>
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Received on Mon Aug 12 2019 - 11:30:03 PDT
