VMD-L Mailing List

From: Eashan C (eashan.chopde_at_gmail.com)
Date: Tue Nov 17 2020 - 20:41:14 CST

Hi,

Thanks for your response!

Unfortunately I’m running into angle parameter errors for SI_3 N_1 SI_3 in
the previous step, I went through the parameter file supplied with the
tutorial, and it seems to be missing the angle parameters for these.

I don’t know if this is a fault in the files that I have downloaded or
whether I have messed up somewhere.

Therefore as the previous step doesn’t execute entirely, I end up not being
able to generate the required eq1.xsc, etc files.

Can anyone help me out with defining the angle parameters for these
specific atoms?

Thanks
Eashan Chopde
Undergrad, BITS Pilani

On Tue, Nov 17, 2020 at 9:36 PM Pang, Yui Tik <andrewpang_at_gatech.edu> wrote:

> Hi Easchan,
>
>
>
> As the error suggested, NAMD cannot find the file eq1.xsc . Are you sure
> you have copy the restart files (I guess they are eq1.coor, eq1.vel and
> eq1.xsc) to the 2_calibrate folder?
>
>
>
> Best,
>
> Andrew
>
>
>
> *From: *Eashan C <eashan.chopde_at_gmail.com>
> *Sent: *Tuesday, November 17, 2020 8:00 PM
> *To: *vmd-l_at_ks.uiuc.edu
> *Subject: *vmd-l: extended system file not found
>
>
>
> Hi,
>
>
>
> Ive been trying to follow the bionanotechnology tutorial to simulate solid
> state nanopores, so far ive gone through the exact same steps as specified
> in the tutorial.
>
>
>
> During the force field calibration, i am required to run namd2 on eq2.namd
> in the 2_calibrate folder for the tutorial.
>
>
>
> However i get an error along the lines of extended system file not found.
> The log file contains the following-
>
>
>
> Charm++: standalone mode (not using charmrun)
>
> Converse/Charm++ Commit ID:
> v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
>
> CharmLB> Load balancer assumes all CPUs are same.
>
> Charm++> Running on 1 unique compute nodes (8-way SMP).
>
> Charm++> cpu topology info is gathered in 0.000 seconds.
>
> Info: NAMD 2.10 for MacOSX-x86_64-multicore
>
> Info:
>
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>
> Info: for updates, documentation, and support information.
>
> Info:
>
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>
> Info: in all publications reporting results obtained with NAMD.
>
> Info:
>
> Info: Based on Charm++/Converse 60601 for multicore-darwin-x86_64
>
> Info: Built Tue Dec 9 15:31:59 CST 2014 by jim on melbourne.ks.uiuc.edu
>
> Info: 1 NAMD 2.10 MacOSX-x86_64-multicore 1
> Eashans-MacBook-Pro.local e
>
> Info: Running on 1 processors, 1 nodes, 1 physical nodes.
>
> Info: CPU topology information available.
>
> Info: Charm++/Converse parallel runtime startup completed at 0.00251102 s
>
> Info: 4210.95 MB of memory in use based on ps
>
> Info: Configuration file is eq2.namd
>
> Info: Working in the current directory
> /Users/e/VMD/bionano-tutorial-files/2_calibrate
>
> TCL: Suspending until startup complete.
>
> Info: EXTENDED SYSTEM FILE eq1.xsc
>
> FATAL ERROR: Unable to open extended system file.
>
>
>
> [0] Stack Traceback:
>
> [0:0] 0 namd2 0x00000001006ff9fd
> CmiAbort + 77
>
> [0:1] 1 namd2 0x000000010007a9ef
> _Z8NAMD_diePKc + 79
>
> [0] Stack Traceback:
>
> [0:0] 0 namd2 0x00000001006fdf79
> charmrun_abort + 249
>
> [0:1] 1 namd2 0x00000001006ffa38
> CmiAbort + 136
>
> [0:2] 2 namd2 0x000000010007a9ef
> _Z8NAMD_diePKc + 79
>
>
>
> Can anyone help me out as to where I might be going wrong? I have gone
> through the tutorial exactly as specified so far, going as far as to
> directly copy the commands from the pdf, rather than type them out on my
> most recent try.
>
>
>
> Thanks
>
> Eashan Chopde
>
> Undergrad, BITS Pilani
>
>
> 

-- 
Eashan Chopde
Department of Sponsorship & Marketing
BITS Pilani,
Pilani.