Acoot Brett wrote:
Here I also mean how can I get the index.npt in the "grompp -f
md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr".
Looking forward to getting your advice.
That file is produced by make_ndx. It is written when you type 'q' and Enter to
quit the program. If you have not specified any other output name, the default
is "index.ndx."
-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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