Hi Dan,
I tried it but I got the following message
> parm hdea.prmtop
Reading 'hdea.prmtop' as Amber Topology
> trajin tassmod4ABstep6_md_reimage.nc
Reading 'tassmod4ABstep6_md_reimage.nc' as Amber NetCDF
> strip ! :90-178 outprefix strip
STRIP: Stripping atoms in mask [:90-178]
Stripped topology will be output with prefix strip
Error: [strip] Not all arguments handled: [ ! ]
> strip !:90-178 outprefix strip
STRIP: Stripping atoms in mask [!:90-178]
Stripped topology will be output with prefix strip
> trajout HdeA_step7_md.inpcrd
Warning: Format not specified and extension '.inpcrd' not recognized.
Defaulting to Amber Trajectory.
Writing 'HdeA_step7_md.inpcrd' as Amber Trajectory
>
On Thu, Sep 28, 2017 at 9:12 AM, Sayuri Pacheco <
sayuri.pacheco.987.my.csun.edu> wrote:
> Hi Dan,
> Thank you I will try that.
>
> -Sayuri
>
> > On Sep 28, 2017, at 9:07 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > On Thu, Sep 28, 2017 at 12:01 PM, Sayuri Pacheco
> > <sayuri.pacheco.987.my.csun.edu> wrote:
> >> Hi,
> >> I used cpptraj to strip certain amino acids from my protein and create
> a new prmtop and .nc file using the following commands.
> >> parm myfile.prmtop
> >> Trajin myfile.nc
> >> Strip ! : 90-178 outprefix strip
> >> Trajout myfile.nc
> >> Go
> >> I was wondering if you can create stripped .inpcrd files in cpptraj?
> >
> > Sure, just do 'trajout myfile.inpcrd restart' after the 'strip'
> > command. See the manual for the full list of supported trajectory
> > formats as well as full syntax for 'trajout'.
> >
> > -Dan
> >
> >>
> >> Sent from my iPad
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
--
Sayuri Pacheco
California State University, Northridge
Biochemistry Major
Undergraduate Biomedical Researcher
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Received on Thu Sep 28 2017 - 15:00:03 PDT
