[gmx-developers] do_dssp bugfix

[David van der Spoel]

Carsten Kutzner wrote:
> Hi,
> 
> we have recently detected a memory problem in do_dssp.
> 
> When do_dssp is given an input pdb containing more than 10 chains,
> memory corruption is likely to appear. This happens because the
> strip_dssp function assumes that the number of lines in the file written
> by the dssp program is equal to the number of residues. However,
> the dssp output file also contains chain separators in separate lines,
> resulting in an extra line per chain.
> 
> For some reason, the affected arrays are currently snewed with (nres+10)
> elements, allowing for 10 separate chains at most. I would suggest to
> snew them with 2*nres-1 elements, allowing each residue to be a
> separate chain at most.
> 
> The allocations that have to be extended are for the variables bb,
> average_area, av_area, norm_av_area, and accri[i].
> 
> Should I immediately fix that in the head and 40 branch?
Yes, please do.

> 
> Carsten
> 
> 
> 
> -- 
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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