[gmx-users] do_dssp

[shahid nayeem]

Hi
No i dont have any capping group
shahid Nayeem


On 5/24/10, Justin A. Lemkul <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>>
>> 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
>
> ========================================
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