From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Dec 03 2015 - 08:50:36 CST
Hi Nancy,
The attached file is a charmm input script not a NAMD configuration
file. From CHARMM-GUI, there ought to be a namd subdirectory, which
contains the actual equilibration files they recommend.
-Josh
On 12/03/2015 08:37 AM, Deng, Jinxia (Nancy) wrote:
>
> Hi All,
>
> I am attempting to run MD of heterogeneous membrane (bilayer lipid).
> All the structures and its input files were generated by Charmm-gui
> interface.
>
> I got six-step input files for equilibration by NAMD (herein attached
> the first input). And I used the below command to launch NAMD, but got
> error (attached below). So just wonder whether you could help me out
> of this. I guess I did not know the right syntax to call program and
> the input files…
>
> _Errors:_
>
> dengj01_at_kzdlpogo2 charmm-gui]$ /sc/kzd/app/x86_64/namd/2.10/namd2
> step6.1_equilibration.inp > test.out &
>
> [1] 7467
>
> [dengj01_at_kzdlpogo2 charmm-gui]$ ------------- Processor 0 Exiting:
> Called CmiAbort ------------
>
> Reason: *FATAL ERROR: wrong # args*: should be "open fileName ?access?
> ?permissions?"
>
> while executing
>
> "open read unit 10 card name step5_assembly.psf"
>
> (file "step6.1_equilibration.inp" line 16)
>
> Charm++ fatal error:
>
> FATAL ERROR: wrong # args: should be "open fileName ?access?
> ?permissions?"
>
> while executing
>
> "open read unit 10 card name step5_assembly.psf"
>
> (file "step6.1_equilibration.inp" line 16)
>
> [1] Abort /sc/kzd/app/x86_64/namd/2.10/namd2
> step6.1_equilibration.inp > test.out (core dumped)
>
> Any of your input is desperately appreciated.
>
> Nancy
>
> *Nancy Deng, Ph.D. *| Principal Scientist, Computational Chemistry &
> Molecular Modeling**
>
> Zoetis Inc| Global Therapeutics Research | 333 Portage Street,
> Kalamazoo, MI 49007
>
> Office:*2693599121 | jinxianancy.deng_at_zoetis.com*
>
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