Hi,
Can you send me off-list the topology and first 10 trajectory frames? Thanks.
-Dan
On Mon, Mar 4, 2019 at 12:15 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> CPPTRAJ: Trajectory Analysis. V18.01
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | 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 5539รข5549.
> [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 - 12:00:02 PST
