[gmx-users] do_dssp

[Justin A. Lemkul]

shahid nayeem wrote:
> Hi
> No i dont have any capping group

Then I have no idea what's going on.  The only data that present a problem are 
in the very first frame, indicating that the HEBT+coil content totals 80 
residues.  All the other frames look fine.  It could be that the algorithm is 
detecting different structural features for the same residue (i.e., they are 
somewhat ambiguous), but I have never heard of such an issue.

-Justin

> shahid Nayeem
> 
>  
> On 5/24/10, *Justin A. Lemkul* <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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> <mailto: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/> <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 <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

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