Hi Dan,
thank you very much for help!
cpptraj has produced valid dcd!
The only question is to
1) how to save subset of atoms in the resulted dcd
for instance I need to save dcd consisted of only protein atoms
:1-361
or
:1-361.CA,N,C -> if I need to save only protein backbone
or
:1-361, Mol -> If I need to save protein +ligand
2) Is it possible to save as the output stripped parm7 file consisted of
topology of protein + ligand only ?
thanks again for help,
James
2015-01-20 19:27 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> You're using cpptraj syntax in a lot of these commands. You need to
> use cpptraj instead of ptraj for this script to work.
>
> On Tue, Jan 20, 2015 at 10:53 AM, James Starlight
> <jmsstarlight.gmail.com> wrote:
> > trajin amd_go.nc 0 last 1
>
> The 'last' keyword for 'trajin' is cpptraj-only. There is no
> equivalent in ptraj. However, since your offset is '1' you can just
> use ' trajin amd_go.nc' and all frames will be read.
>
> > # fitting to protein
> > center :1-361 mass origin
> > image origin center
>
> For most cases, 'autoimage' is the recommended command for imaging
> instead of 'center'/'image' (again, cpptraj only).
>
> > trajout md_proc.dcd dcd nobox
>
> The 'dcd' keyword is cpptraj-only. For DCD output with ptraj, only the
> 'charmm' keyword works. If you look at your output it likely says it's
> defaulting to Amber trajectory format here.
>
> My recommendation is to just use cpptraj (from AmberTools 14) since
> ptraj is no longer actively developed.
>
> -Dan
>
> >
> > ! in fact
> > 1) it produce again full system trajectory without stripping the solvent
> > 2) broken dcd file (is not recognized by VMD) but there is no problem if
> I
> > chose netCDF output again
> >
> >
> > Thanks for help,
> >
> > James
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Wed Jan 21 2015 - 06:00:05 PST
