[gmx-users] on Umbrella Sampling
acootbrett at yahoo.com
Sun Apr 1 15:01:51 CEST 2012
The original PDB file (2BEG) has 5 chains. In your tutorial you fix chain B. Thus if I am right, the energy calculated should be the disintegation energy of the whole protein to the 5 chain peptide. In addition the protein chain in the original pdb is from residue 17 to 42.
This makes me confused when you define "1-27" to chain A, and "28-54" to chain B.
It seems your tutorial protein is a 2 chain protein, not the 5 chain protein.
Can you give me further clarification?
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, 1 April 2012 10:49 PM
Subject: Re: [gmx-users] on Umbrella Sampling
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."
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> *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?
> -- ========================================
> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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