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* <jalem...@vt.edu
<mailto:jalem...@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* <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@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
========================================
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