I'm travelling until wed. so I dont have code access until then, but the
problem is that including velocity info is relatively new and the original
imaging routines only ever had to deal with coords. I suspect that
unfortunately this will need a bugfix. I will let you know when I get back.
-Dan
On Saturday, August 31, 2013, Eric Berquist wrote:
> AmberTools 13 up to bugfix 16, and cpptraj v13.15.
>
>
> On Sat, Aug 31, 2013 at 7:14 AM, Daniel Roe <daniel.r.roe.gmail.com<javascript:;>>
> wrote:
>
> > Hi,
> >
> > What version of cpptraj are you using?
> >
> > -Dan
> >
> > On Friday, August 30, 2013, Eric Berquist wrote:
> >
> > > I need to reimage a trajectory with velocity information in order to
> > spawn
> > > QM/MM trajectories from it at various points. However, when I
> autoimage,
> > > cpptraj explicitly tells me the resulting trajectory doesn't have
> > velocity
> > > information. Is there any way of fixing this without going in and
> > modifying
> > > the code myself?
> > >
> > > The relevant parts of the cpptraj output follow:
> > >
> > > INPUT: Reading Input from STDIN
> > > [trajin 1e1a.04.md_prod_nvt.nc]
> > > [1e1a.04.md_prod_nvt.nc] contains 25000 frames.
> > > [autoimage anchor .9045]
> > > AUTOIMAGE: To box center based on center of mass, anchor mask is
> > > [.9045]
> > > [trajout 1e1a.04.md_prod_nvt_imaged.nc]
> > >
> > > PARAMETER FILES:
> > > 0: 1e1a.prmtop, 99260 atoms, 30638 res, box: Trunc. Oct., 30094 mol,
> > 30063
> > > solvent, 25000 frames
> > >
> > > INPUT TRAJECTORIES:
> > > 0: [1e1a.04.md_prod_nvt.nc] is a NetCDF AMBER trajectory containing
> > > velocities, Parm 1e1a.prmtop (Trunc. Oct. box) (reading 25000 of 25000)
> > > Coordinate processing will occur on 25000 frames.
> > >
> > > REFERENCE COORDS:
> > > No frames defined.
> > >
> > > OUTPUT TRAJECTORIES:
> > > [1e1a.04.md_prod_nvt_imaged.nc] is a NetCDF AMBER trajectory, Parm
> > > 1e1a.prmtop: Writing 25000 frames (1-Last, 1)
> > >
> > >
> > > Eric Berquist
> > > Lambrecht Group
> > > University of Pittsburgh
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;> <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Aug 31 2013 - 15:00:03 PDT
