Sorry - I had forgotten that selection by distance requires a reference
structure (for further details see the reference manual). Just add a
‘reference nvt10.ns.rst7’ after the ‘parm’.
Hope that helps,
-Dan
On Wed, Aug 14, 2019 at 5:32 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> Well, it seemed fully logical and this is likely shell related. Sadly, I
> seem unable to figure out how to get the suggested command sequence to
> execute correctly
>
> The
>
> strip "!((:1 <: 5) & ! :1)"
>
> command produces an error:
>
> No reference set, cannot select by distance
>
> Meaning that I get the "guest" file correctly and I do get the “host”
> file, however the only thing striped is :1 and every other molecule is
> there. I have tried varying or skipping “ and ‘ though this produces other
> errors where all of the mask is not read or I have “unmatched” parenthesise
> though I cannot see this in the commands.
>
> I have pretty much tried every combination of apostrophes and escape
> characters I can remember without any luck so once again I am looking for
> some input from people smarter then me.
>
> Best regards
> // Gustaf
>
>
>
> > On 12 Aug 2019, at 20:05, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > 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 Wed Aug 14 2019 - 05:00:02 PDT
