[gmx-users] do_dssp

[Justin A. Lemkul]

shahid nayeem wrote:
> Hi Justin
> I choose group 5 main chain for dssp calculation

Do you have any capping groups (N-acetyl, C-amine, etc)?

-Justin

> Shahid Nayeem
> 
>  
> On 5/24/10, *Justin A. Lemkul* <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     shahid nayeem wrote:
> 
>         Dear All
>         I did 10ns simulation of three peptide residue solvated in
>         water. Each peptide residue is 26 residue long. In final .gro
>         file it is showing total 78 residue which is O.K. as 3x26=78.
>         For inserting three similar peptide I used genconf command. when
>         I run dssp I get total residue as 80. The command for dssp is
>         do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
>         output of dssp run is as follows.
> 
> 
>     When prompted, what group did you choose for the analysis?
> 
>     -Justin
> 
> 
>         @ s0 legend "Structure"
> 
>                
> 
>         @ s1 legend "Coil"
> 
>                        
> 
>         @ s2 legend "B-Sheet"
> 
>                
> 
>         @ s3 legend "B-Bridge"
> 
>                
> 
>         @ s4 legend "Bend"
> 
>                        
> 
>         @ s5 legend "Turn"
> 
>                        
> 
>         @ s6 legend "A-Helix"
> 
>                
> 
>         @ s7 legend "5-Helix"
> 
>                
> 
>         @ s8 legend "3-Helix"
> 
>                
> 
>               0    46    24     0     0     7    10    36     0     3
> 
>              10    39    26     0     0    15     4    35     0     0
> 
>              20    37    29     0     0    11     4    33     0     3
> 
>              30    37    32     0     0    11     2    35     0     0
> 
>              40    36    31     0     0    10     6    30     0     3
> 
>              50    41    30     0     0     9    10    31     0     0
> 
>         Please suggest why I am not getting the actual number of residue
>         in dssp file.
>         When I follow the same procedure for full protein molecule
>         simulation I get the same number of residue in dssp output as
>         well as final.gro file
>         shahid nayeem
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================