Acoot Brett wrote:
I have type the help at the prompt of make_ndx, but it does not give the
explaination as I expected. Thus I hope you can give me an explaination
based on your tutorial.
What were you expecting that you didn't get? The help information describes all
of the sytax. For instance, it contains the following lines:
'name' nr name : rename group nr to name.
...
'r' nr1 - nr2 : selects residues in the range from nr1 to nr2.
...
'q' : save and quit.
Those lines alone directly answer your questions.
-Justin
Cheers,
Acoot
*From:* Justin A. Lemkul <[email protected]>
*To:* Acoot Brett <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*Sent:* Sunday, 1 April 2012 10:32 PM
*Subject:* Re: [gmx-users] on Umbrella Sampling
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
========================================
--
========================================
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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