On Thu, Aug 9, 2018 at 1:31 PM Simon Kit Sang Chu
<simoncks1994.gmail.com> wrote:
>
> Hi Dave,
>
> I did the following instead.
>
> cpptraj -p file.prmtop -y file.rst
>
> strip !:@CA
>
> write file.pdb
>
> I guess command "write" is not compactable with strip here. Please correct
> me if I am mistaken.
The 'write' command is for writing data sets. The 'trajout' command is
for output trajectories. See the manual for full details on these
commands.
-Dan
>
> Sorry for the unclear inquiry.
>
> Regards,
> Simon
>
> Daniel Roe <daniel.r.roe.gmail.com> 於 2018年8月10日週五 上午12:24寫道：
>
> > Hi,
> >
> > On Thu, Aug 9, 2018 at 12:05 PM Simon Kit Sang Chu
> > <simoncks1994.gmail.com> wrote:
> > > Is there an option to cpptraj write / ambpdb only selected atoms in
> > > rst (CDF format)?
> > >
> > > strip command in cpptraj seems to only alter the topology file and the
> > > outputted pdb still contains the stripped atoms.
> >
> > In the future it's better if you report the exact input you used with
> > cpptraj - that helps us get a better idea of what may be going wrong.
> >
> > The 'strip' command will modify both the topology and coordinates. If
> > I wanted to write a PDB containing only CA atoms for example, I might
> > use something like the following input:
> >
> > parm myparm.parm7
> > trajin mytraj.nc
> > strip !.CA parmout strip.parm7
> > trajout strip.nc
> >
> > After this, strip.nc will contain only atoms named CA, and strip.parm7
> > will be the corresponding stripped topology.
> >
> > Hope this helps,
> >
> > -Dan
> >
> > >
> > > Thanks,
> > > Simon
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Received on Thu Aug 09 2018 - 11:30:04 PDT
