[gmx-users] do_dssp

[Justin A. Lemkul]

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 
> 

-- 
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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

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