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
> _______________________________________________
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> 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 - 04:30:02 PDT
