[gmx-users] do_dssp

[shahid nayeem]

Hi Justin
I choose group 5 main chain for dssp calculation
Shahid Nayeem


On 5/24/10, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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