From: Deng, Jinxia (Nancy) (jinxianancy.deng_at_zoetis.com)
Date: Thu Dec 03 2015 - 09:52:20 CST
Thank you all for the advice, now it is running when I use the right input from the subfolder: namd ☺
Nancy
From: Chitrak Gupta [mailto:chgupta_at_mix.wvu.edu]
Sent: Thursday, December 03, 2015 9:50 AM
To: NAMD list; Deng, Jinxia (Nancy)
Subject: Re: namd-l: error when use Charmm_Gui prepared *.inp for NAMD
Hi Jinxia,
Looks like you were trying to run a charmm input file using NAMD.
I have used charmm-gui.org<http://charmm-gui.org> website to generate my inputs. They usually provide a set of NAMD input files along with charmm input files (these would usually be in a separate "namd" folder). Try with that, it should work.
Best,
Chitrak.
On Thu, Dec 3, 2015 at 9:37 AM, Deng, Jinxia (Nancy) <jinxianancy.deng_at_zoetis.com<mailto:jinxianancy.deng_at_zoetis.com>> 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<tel:2693599121> | jinxianancy.deng_at_zoetis.com<mailto:jinxianancy.deng_at_zoetis.com>
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