From: Chris Harrison (charris5_at_gmail.com)
Date: Wed May 09 2012 - 16:21:02 CDT
Dear Caitlin,
Can you send me the file off-list?
Best,
Chris
On Wed, May 9, 2012 at 1:05 PM, Caitlin Scott <cescott_at_caltech.edu> wrote:
> Hi NAMD Users,
>
> When I run the multicore executable
> (NAMD_2.9_Linux-x86_64-multicore/namd2)
> ERROR lines appear in my log file:
> Info: 197 VDW
> Info: 0 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> Info: TIME FOR READING PSF FILE: 0.882767
> Info: TIME FOR READING PDB FILE: 0.119342
>
> I assume there's a problem reading the psf file. When I run this same job
> with a different executable
> (NAMD_2.6_Linux-i686-TCP/namd2) I don't get the ERROR lines:
> Info: 197 VDW
> Info: 0 VDW_PAIRS
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 48162 ATOMS
>
> How do I fix this? I would attach the psf file, but it's very large. Is
> there a certain part of the psf file I should refer to?
>
>
> Thanks in advance.
>
> Caitlin Scott
>
>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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