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> 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:;>
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Aug 31 2013 - 08:00:02 PDT
