Dear AMBER Users,
I want to strip water and ions from md.mdcrd file (10000 frames) in cpptraj
and I used the following script. My job is killed after the 10-40% of
completion. I request you to kindly help me to fix this error.
trajin md.mdcrd
autoimage
strip :WAT,Cl-,Na+ outprefix stripped
trajout md_dry.mdcrd
Error:
PARAMETER FILES:
0: 'com_solvated.top', 15805 atoms, 4008 res, box: Orthogonal, 3725 mol,
3721 solvent, 10000 frames
INPUT TRAJECTORIES:
0: 'md.mdcrd' is an AMBER trajectory, Parm com_solvated.top (Orthogonal
box) (reading 10000 of 10000)
Coordinate processing will occur on 10000 frames.
OUTPUT TRAJECTORIES:
'md_dry.mdcrd' is an AMBER trajectory, Parm com_solvated.top: Writing
10000 frames (1-Last, 1)
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'com_solvated.top' (2 actions):
0: [autoimage]
Anchor molecule is 1
The following molecules are fixed to anchor: 2
3723 molecules are mobile.
1: [strip :WAT,Cl-,Na+ outprefix stripped]
Stripping 11165 atoms.
Stripped parm: 'com_solvated.top', 4640 atoms, 285 res, box:
Orthogonal, 2 mol
Writing topology 0 (com_solvated.top) to
'stripped.com_solvated.top' with format Amber Topology
----- md.mdcrd (1-10000, 1) -----
0% 10% 20% 30% Killed
*Thanks & Regards*
*Ramesh M*
Email: shreeramesh.gmail.com Mob.: +91-9542200332
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Received on Mon Jul 06 2020 - 09:30:02 PDT
