Hi Wei,
> I was trying to run the script run_MDEQ.sh, but it is missing a
> file "fixedgroups".
> Can you send the other file so I can reproduce the error?
The person I was working with who saw this problem and provided me with the
scripts did not include this. However, it is not needed to see the issue.
Just remove it from the script and set ntr=0.
> and I agree with Jason and Lachele that the problem seems to be with
> the section "SOLVENTS_POINTER"
I agree, I think the two most likely culprits are the solvent pointers and
the section that defines the atoms per molecule. The real problem occurs
when one has glycans bound to the protein. Then both sander and pmemd image
the glycan without imaging the rest of the molecule and things blow up
because you end up with hugely stretched bonds. This to me looks like the
glycans are not placed in the same molecule as the protein but I haven't had
time to sit and properly look at it.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Apr 08 2011 - 12:00:13 PDT
