shahid nayeem wrote:
Dear Mark
Following your advice I started using three peptide in one simulation
box. Iwas able to add these with genconf as previously in ordered
manner, generated .gro with genconf, solvated it and after energy
minimization I did MD run for 10ns. Everything ran well. In the end when
I see the trajectory I find unfolding of the original chain but the two
additional peptide introduced through genconf show appearance of new
secondary structures. Even in these two the secondary structure do not
develop at the same point. Why the three equivalent peptide behave
differently in similar environment. How can I explain this observation.
why the first peptide does not show any new secondary structure. Sholud
I go with higher number of molecule. Will it make any difference if
peptides are added in disordered manner and then simulated.
Initial orientation should likely have nothing to do with it. Perhaps this is
even the proper behavior for whatever your peptide is. Is its structure
dynamic? Is the size of your peptides large enough to even believe that they
would be intrinsically stable? Many model peptides, in isolation, have very
transient structures.
It could also be that your simulation parameters are poorly chosen, so the force
field is breaking down. If you want comments on your .mdp file, please post it.
-Justin
Shahid
On 4/23/10, *Mark Abraham* <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 23/04/10 13:16, shahid nayeem wrote:
Dear All
I am trying to study inter peptide interaction fpr which I need
to put
more than one peptide in one simulation box. I did it with genconf
command but this inserts peptide in a regular ordered manner I want
these to be in irregular disordered insertion. Even after using
genconf
Well that's a difficult and atypical scenario. genconf -shuffle will
allow you to stack the same peptide in a regular array with random
rotations of the whole box. Then you can solvate, equilibrate and
run MD at a high temperature to give yourself a quasi-disordered
starting state.
, I tried to proceed furthe after solvation with spc water. The
energy
minimization (steepest descent) failed to converge even after
5000 steps
and theirafter position restraint dynamics failed giving
segmentation
fault. Introducing more peptide after generating .gro with -ci -nmol
gives error showing more than one residue in insert molecule.
Please help me and write commands which I should follow.
No, because that's an impossible task. We can't begin to guess the
reasons for things failing without seeing the actual output (was the
EM energy large and negative? what was the actual error message
from -ci -nmol?).
You should be careful to start with a small test case so that you
can learn the workflow with a manageable problem. Can you get a
single peptide to equilibrate? Two stacked peptides? It is best to
learn to walk before trying to run :-)
Mark
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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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