Re: [AMBER] Strip water job is killed after 10-40% completion

From: Dr. Anselm Horn <anselm.horn.fau.de>
Date: Tue, 7 Jul 2020 16:08:38 +0200

Dear Ramesh,

you could place the strip command before the autoimage command in your
input to avoid imaging all your water molecules in the trajectory that
are deleted thereafter anyway. Maybe this helps.

Regards

Anselm



On 07/06/2020 06:23 PM, Shreeramesh wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Tue Jul 07 2020 - 07:30:02 PDT
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