From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Thu Dec 03 2015 - 08:44:53 CST
Hi Nancy,
It looks like you are using the wrong input file. This input file
is written for the CHARMM simulation engine. There should be another
directory produced by CHARMM-GUI that has NAMD formatted input files.
Regards,
Jeff
-- Jeffrey Potoff Professor & Director of Early Engineering Programs Department of Chemical Engineering and Materials Science Wayne State University http://potoff1.eng.wayne.edu http://gomc.eng.wayne.edu On 12/3/2015 9:37 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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