Acoot Brett wrote:
Dear All,
In the on-line tutorial "Umbrella Sampling " by*Justin Lemkul in
"http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html"* ,
there is a command "grompp -f md_pull.mdp -c npt.gro -p topol.top -n
index.ndx -t npt.cpt -o pull.tpr". Here is the index.ndx exactly same as
following?
make_ndx -f npt.gro
(> indicates the make_ndx prompt)
> r 1-27
> name 19 Chain_A
> r 28-54
> name 20 Chain_B
> q
Then what is the meaning of "r1-27", what is the meaning of " name 19
Chain_A", and what is the meaning of "q"?
Type "help" at the make_ndx prompt for an explanation.
Suppose I have a protein-peptide complex A, the protein is of 400
aas,the peptide is 20 aas. Suppose I have another protein-peptide complx
B, and the only difference beteen protein complex A and complex B is
that in position 3 of peptide of complex A, it is Ala. In the
coresponsing position of the peptide of complex B, it is Arg.
Can the results of this Umbrella Sampling calculation be accurate enough
to show that the binding energy between the protein and peptide in
complex A and B is different and cuurently reflects the fact that the
difference is caused by the substitution of Ala by Arg?
Probably.
-Justin
--
========================================
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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