[gmx-users] do_dssp

[singh]

Dear Gromacs users,

As I am simulating many peptides in a box and do_dssp is only a wrapper for
calling the program which works on pdb files, I was of the view that it will
not take PBC into consideration and will probably not assign beta sheets
very well. Please correct me if I am wrong.
If this is the case, Is there any other way to assign secondary structure to
such a system?

Regards,
Gurpreet Singh 




On 12/21/06, singh <singh at biophysik.chemie.uni-dortmund.de> wrote:
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> Dear Gromacs users,
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> I have simulated 12 peptide fragments in a cubic box and I want to use
> do_dssp for secondary structure analysis but I am not sure whether
Periodic
> boundary conditions will be taken in account during assignment
(particularly
> for assigning betasheets).
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> Regards,
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> Gurpreet Singh
>
> -------------------------------------------------
>
> University of Dortmund
>  Department of Chemistry
>  Physical Chemistry I  -  Biophysical Chemistry
>  Otto-Hahn Str. 6
>  D-44227 Dortmund
>  Germany
>  Office:   C1-06 room 176
>  Phone:  +49 231 755 3916
>
> Fax:     +49 231 755 3901
>
> -------------------------------------------------
But there could be a problem for beta sheets between different chains and
for crystal contacts.

--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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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Hi Gurpreet,

The common message is "don't worry, mdrun doesn't write broken
molecules". So you're secondary structure will not be affected by
periodic boundary conditions.

Cheers,

Tsjerk