CPPTRAJ: Trajectory Analysis. V18.01
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| Date/time: 03/04/19 12:13:49
| Available memory: 1.120 GB
INPUT: Reading input from 'run.in'
[parm ./setup/ACN_IL1B_solvated.prmtop]
Reading './setup/ACN_IL1B_solvated.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin ./run_1/prod/ACN_IL1B_production4H.mdcrd]
Reading './run_1/prod/ACN_IL1B_production4H.mdcrd' as Amber NetCDF
[spam purewater name SPAM cut 12.0 out spampure.dat]
SPAM:
Calculating bulk value for pure solvent
Printing solvent energies to spampure.dat
Data set 'SPAM' index is water # * frame.
Using a 12.00 Angstrom non-bonded cutoff with shifted EEL.
#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; "SPAM: A Simple Approach
# for Profiling Bound Water Molecules"
# J. Chem. Theory Comput., 2013, 9 (12), pp 5539â5549.
[avg SPAM out spam.avg.dat name AVG]
AVERAGE: Calculating average of 1 data sets.
Data set base name 'AVG'
Output to to 'spam.avg.dat'
[go]
**************************************************************************************************************************************************************************
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: ACN_IL1B_solvated.prmtop, 39605 atoms, 12325 res, box: Orthogonal, 12173 mol, 11955 solvent
INPUT TRAJECTORIES (1 total):
0: 'ACN_IL1B_production4H.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
Coordinate processing will occur on 1250 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'ACN_IL1B_solvated.prmtop' (1 actions):
0: [spam purewater name SPAM cut 12.0 out spampure.dat]
Found 11955 solvent residues [WAT]
Total Grid memory: 8.419 MB
TIME: Pair List Setup: 0.0186 s
Grid dimensions: 17 19 18 (5814 total).
----- ACN_IL1B_production4H.mdcrd (1-1250, 1) -----
0% *** Error in `cpptraj': munmap_chunk(): invalid pointer: 0x0000000002883f20 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5d4)[0x7f3a7cdd05d4]
cpptraj[0x484ecc]
cpptraj[0x502b7c]
cpptraj[0x41058e]
cpptraj[0x5d2e0e]
cpptraj[0x5d3508]
cpptraj[0x71ab7f]
cpptraj[0x71b16b]
cpptraj[0x71f1c0]
cpptraj[0x72423f]
cpptraj[0x7269e9]
cpptraj[0x726e78]
cpptraj[0x40fd23]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f3a7cd733d5]
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Received on Mon Mar 04 2019 - 09:30:02 PST
