From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Thu Dec 03 2015 - 08:44:53 CST
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.
-- 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 & > >  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) > >  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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