[gmx-users] Martini force field: elastic network
Hualin.Li at uth.tmc.edu
Fri Oct 14 19:11:30 CEST 2011
Thank you for your reply. The method I used is from previous tutorial, which goes like this:
" Martini + simple elastic network
The first option to help preserve higher-order structure of proteins is to add to the standard Martini topology extra harmonic bonds between non-bonded beads based on a distance cutoff. Note that in standard Martini, long harmonic bonds are used to impose the secondary structure of extended elements (sheets) of the protein.
1. Generate a coarse-grained PDB structure you want to use as the reference structure.
2. Generate a list of distances between all beads within a certain distance.The GROMACS tool genrestr is well suited for this. First generate an index file containing only those beads you want to consider, the standard option would be the backbone beads.
genrestr -f cg.pdb -n index -constr -o constraints
3. Select those restraints you want to keep, based on a lower and upper cutoff. In adding to Martini you would not want to duplicate already existing bonds, so the ”select restr.pl” script (protein_tutorial.tar.gz) includes a lower cut-off value. The example below selects all instances from the full list in ”constraints.itp” with a distance between 0.5 and 0.9 nm and generates a harmonic bond with a force constant of 500 kJ mol-1 nm-2.
./select_restr.pl constraints.itp 0.5 0.9 500 > AddElBonds.itp
4. Paste the resulting file into the standard Martini topology for the protein (protein.itp) in the section [ bonds ].
5. Proceed as before and start a production run."
If there is any problem, what is the problem please? In the new script martinize.py, when typing "martinize.py -h" , this description show up
Elastic network: Fij = Fc exp( -a (rij - lo)**p )
-elastic Write elastic bonds (not working yet)
-elnedyn Use Elnedyn mapping and parameters with elastic network
-ef Elastic bond force constant Fc
-el Elastic bond lower cutoff: F = Fc if rij < lo
-eu Elastic bond upper cutoff: F = 0 if rij > up
-ea Elastic bond decay factor a
-ep Elastic bond decay power p
-em Remove elastic bonds with force constant lower than this
-eb Comma separated list of bead names for elastic bonds
-cgo PyMOL CGO file for elastic network visualization
Is my understanding about the line " -elastic Write elastic bonds (not working yet) " verbally wrong or it is already working please?
Thank you very much for your reply? Is there any way to get the old version of select_restr.pl please?
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of XAvier Periole [x.periole at rug.nl]
Sent: Friday, October 14, 2011 11:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Martini force field: elastic network
The website has been updated to fit a CG tutorial starting monday in
The manner of the construction you describe in your email is not the
proper way to do it!
The new script is doing it properly.
If you want the old script to only generate the elastic network (as it
seems from your email) you may have it or use the scripts from the
On Oct 14, 2011, at 5:58 PM, Li, Hualin wrote:
> Dear all,
> I am using martini force field to generate elastic network
> for my protein. I generate a list of distance between all beads
> within a certain distance by:
> genrestr -f ***.gro -n index.ndx -constr -o constraints
> getting the constraints.itp file and will continue with the
> 2nd step by using a script:
> ./select_restr.pl constraints.itp 0.5 0.9 500
> However, the martini forcefield developer seems to update
> their website yesterday and I can't find the select_restr.pl any
> more and in the new script they provide ( martinize.py), -elastic
> to write elastic bonds is not working yet. Could some one provide
> me the old script "select_restr.pl" please?
> Many thanks.
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