On Mon, 2014-05-12 at 11:53 +0000, Valentina Romano wrote:
> Yep.
>
> I didi it. And this is the result:
>
> CPPTRAJ: Trajectory Analysis. V13.22
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> AmberParm Title: [default_name]
> Radius Set: modified Bondi radii (mbondi)
> INPUT: Reading Input from file PknGAde-wt-min.check_overlap
> [trajin PknGAde-wt-min.rst]
> [PknGAde-wt-min.rst] contains 1 frames.
> [checkoverlap]
> CHECKSTRUCTURE: Checking atoms in mask [*].
> Checking inter-atom and bond distances.
> Warnings will be printed for bond lengths > eq + 1.15 Ang
> and non-bond distances < 0.80 Ang.
> [go]
>
> PARAMETER FILES:
> 0: PknGHAdeH_ion_wt.prmtop, 28424 atoms, 8443 res, box: Orthogonal, 8198 mol, 8190 solvent, 1 frames
>
> INPUT TRAJECTORIES:
> 0: [PknGAde-wt-min.rst] is an AMBER restart file, no velocities, Parm PknGHAdeH_ion_wt.prmtop (Orthogonal box) (reading 1 of 1)
> Coordinate processing will occur on 1 frames.
>
> REFERENCE COORDS:
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM [PknGHAdeH_ion_wt.prmtop] (1 actions):
> 0: [checkoverlap]
> CHECKSTRUCTURE: * (28424 atoms, 28459 bonds), imaging on.
> ----- [PknGAde-wt-min.rst] (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> No data sets.
>
> Thus apparently there are no clashes in the minimizaed structure.
>
> If both energy and overlaps are fine in my starting structure, how can
> i understand why the MD is not working properly?
>
> Any idea?
Did you try my suggestions?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 12 2014 - 06:30:02 PDT
