Kirill Bessonov wrote:
I was giving today my poster presentation and one of profs from my
department was very critical on the fact that my peptide is drifting or
moving along the DMPC bilayer. Watch video of 100ns simulation here:
He said that is unprobable, I want to know if this is some kind of
artifact (i.e. system is diffusing). I had DMPC molecules displaying
artifacts, so I converted trajectory with
trjconv -pbc mol -ur compact
I would argue that it would be physically unrealistic to see a peptide *not*
drift along the bilayer. To compare, use g_msd to calculate the lateral
diffusion coefficient of both the peptide and the lipids. If they are
comparable, the peptide is simply drifting along with the lipids.
Another question: I want to start simulation of a pepetide that has
non-natural amino acid (Azetidine -2 - carbpxylic acid, AZE in short).
The only structural difference is that proline has 5 membered ring and
AZE only 4. Therefore I was wondering if it is at all possible to
simulate that kind of peptide, since I expect complains from grompp
about amino acid name, AZE not being in its database. Please advise on
how to approach this problem
Add AZE to the force field's .rtp and .hdb file, and use pdb2gmx. It should be
fairly straightforward to define this residue based on the building blocks
present in the force field, especially if you're using a Gromos parameter set.
-Justin
Thanks
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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