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?
Vale
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Monday, May 12, 2014 1:47 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Analysis of minimization stage
On Mon, May 12, 2014, Valentina Romano wrote:
> I would like the use cheackoverlap in cptraj but is not really clear how
> it works.
We probably don't emphasize enough the help facility in cpptraj, e.g.:
in cpptraj, typing "help checkoverlap" will give you usage. In this case
is quite simple:
parm <parmtop-file>
trajin <restart file from minimization>
checkoverlap
go
Hope this helps....dac
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Received on Mon May 12 2014 - 05:00:05 PDT
