Sorry it worked. Thank you for your help.
On Thu, Sep 28, 2017 at 2:52 PM, Pacheco, Sayuri <
sayuri.pacheco.987.my.csun.edu> wrote:
> 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
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> 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
>
--
Sayuri Pacheco
California State University, Northridge
Biochemistry Major
Undergraduate Biomedical Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 28 2017 - 15:00:04 PDT
