From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 24 2008 - 10:37:34 CDT
Hi Eva,
when you say that the minimization stalls, how long did you wait? Did it
crash or just hang? Also, when you built your structure, do you see any
exceptionally long bonds, or atoms located at (0,0,0)? Either of these
can happen when you're building from an incomplete structure (which it
appears you are), and can cause problems during minimization.
Best,
Peter
Eva Nong wrote:
> Dear all,
>
> I generated a PSF file using a gedit text file and tried to account
> for as many missing atoms as I could and split the protein and DNA
> chains before sending it to energy minimization. But the min.out file
> seemed to stall after the 1st step without leaving me with any
> error/warning messages. The out file for PSF and minimization are
> listed as below, respectively:
> PSF out file:
> www.hcs.harvard.edu/~prisemag/eva/files/3ktqchain.out
> <http://www.hcs.harvard.edu/%7Eprisemag/eva/files/3ktqchain.out>
> Min out file:
> www.hcs.harvard.edu/~prisemag/eva/files/min3ktqchain.out
> <http://www.hcs.harvard.edu/%7Eprisemag/eva/files/min3ktqchain.out>
> Can you please help me out?
>
> Thanks much
>
> Eva
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