Re: error in scripting

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Tue Feb 16 2010 - 11:51:03 CST

To follow up on Axel's post, getting a bilayer system started can be
somewhat difficult. We have found that CHARMM_GUI
http://www.charmm-gui.org/
produces starting configurations for lipid bilayers that are reasonably
well minimized/equilibrated such that one can initiate heating and
dynamics without much effort.

Your output also suggests that your PSF file might have some errors in
it (missing patch).
Regards,
    Jeff

ipsita basu wrote:
> Dear all,
> I have prepared a bilyer in charmm and make psf file in
> xplor format. I want to minimise and then equilibrate it in namd. But
> the job is aborted. My input is attached here and some of the errors
> are given below:
> ERROR: Stray PME grid charges detected: 1 sending to 3 for planes 97 98 99
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
> Warning: Bad global dihedral count!
> Warning: Stray PME grid charges ignored!
> PRESSURE: 2321 1.74905e+10 -2.63334e+09 -1.65952e+10 -2.63334e+09
> 4.97756e+08 2.54818e+09 -1.65952e+10 2.54818e+09 1.58308e+10
> GPRESSURE: 2321 1.74926e+10 -2.63287e+09 -1.65934e+10 -2.63338e+09
> 4.98307e+08 2.54861e+09 -1.65959e+10 2.54445e+09 1.58289e+10
> ENERGY: 2321 58066783.1514 6197301.7556 5003.8692 331.3541
> -93129.8653 99999999.9999 0.0000 0.0000 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000
> 99999999.9999 99999999.9999 799507.5942 99999999.9999 99999999.9999
>
> ERROR: Stray PME grid charges detected: 0 sending to 2 for planes 50
> 51 54 55 56 57
> ERROR: Stray PME grid charges detected: 1 sending to 3 for planes 79
> 80 81 82 83 84 85 86 87 88 89 90 91 92 93
> Warning: Tuple 5033 with atoms 5063(23) 5066(41) missing patch 41
> FATAL ERROR: Patch needed for tuple is missing.
>
> Stack Traceback:
> [0] [0x8246780]
>
> Can you please suggest me what is the solution of it? I read such
> problems in namd-mailing list and according to some thread I increase
> pmegridsize. But doing this the job is running for few steps more but
> aborted finally. Please give me some suggestions.
>
>
> Thanking You
>
> Ipsita Basu
>
>
>
>
>
>
>

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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