abdullah ahmed wrote:
Hello everyone,
I have two protein structures, and the insides of both are not exposed
to water.
One structure contains two oppositely charges residues (GLU and LYS)
facing each other. The second structure contains a GLU residue only.
Upon minimization I had expected the coloumb energies of the first
structure to be lower than that of the second. However, this was not the
case, they are both very similar.
Does anyone have an idea as to why this has happened?
(The only explaination I can come up with is that perhaps the effect is
so small that it can not be seen)
We discussed this at length yesterday. By doing a simple energy minimization
(in which, if I recall, you are applying position restraints), you stand to
prove very little. By doing MD and obtaining an ensemble of energies, you stand
a better chance of calculating a relevant energy.
I was not sure if providing PDB and .mdp files would be helpful, but I
can send then in my next mail if neccesary.
The .pdb file is unnecessary. Only post the .mdp file if it has changed since
the one you posted yesterday.
-Justin
Thank you in advance!
Abdullah Ahmed
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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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