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Tutorial on Sugars
- robrob2013
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However, I dont know how I could produce a CG gro file of MALTOHEPTAOSE.
I have already checked the extension file of sugars (martini_v2.0_sugars.itp)
but still I'm clueless on how to start with this.
is there a tutorial that deals with the basics of dealing something like this?
Thank you everyone!
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- Clement
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Nope, sadly we do not have such tutorial. At least not on sugar specifically. But by comparing the AA structure of your molecule and how the CG models are derived from simpler sugars, you can come up with something. If my eyes serve, I'd say your maltoheptaose is just a polymer of seven glucose molecules; you can check and compare to the maltose structure (polymer of two glucose molecules) in the sugar .itp file to have an idea of how to build a more complex sugar...
Do not hesitate to post intermediary steps here...
Good luck!
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- siewert
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Generating a starting gro file is easy - putting the right amount of constituting CG beads randomly in a box could already serve as a suitable starting coordinates file, as Martini molecules are very easily energy minimized.
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- sruthip
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Where am I going wrong? Please suggest.
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- cm
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- vainikka
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Refrain from asking the same question in multiple threads.
As for your issue: See the GROMACS manual about 'insert-molecules':
manual.gromacs.org/documentation/current...nsert-molecules.html
There are other options available as well, such as PACKMOL.
If at any point you are unsure about what you are doing, check out the GROMACS tutorials, and if you have further questions that are only related to the use of GROMACS, go check out their forum. It is highly likely that the question you have has already been answered.
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- cm
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- cm
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I am now able to insert the all atom pdb of trehalose in the coarse grained water box.
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- vainikka
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Unless you are running some sort of hybrid CG/AA simulations, the atomistic structures should not be in the same box with CG structures.
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- cm
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Fatal error:
DD cell 1 0 0 could only obtain 84 of the 86 atoms that are connected via constraints from the neighboring cell. This probably means your constraint length are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order.
i have tried with -rdd 1.4 option, but it still does not working.
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- vainikka
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For minimization of far-out-of-equilibrium systems, you can comment out the constraints and remove the comment symbols (';') on the bonded parameters.
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- cm
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grompp -f minimization.mdp -c system-solvated.gro -p system.top -o minimization.tpr -maxwarn 1
but during this below command:
mdrun -deffnm minimization -v
i am getting the error.
My system consist of
Protein_A 2
W 11357
CL- 16
TREH 20
"For minimization of far-out-of-equilibrium systems, you can comment out the constraints and remove the comment symbols (';') on the bonded parameters." Can you please explain this, i am not getting your point.
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- vainikka
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Anything after that symbol is not read by GROMACS.
In the Martini2 sugar topologies trehalose uses constraints, and lines defining bonds are commented out (i.e. the lines start with the symbol ';').
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- cm
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Does it will make any problem in further simulation, as i have remove the constrain.
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- vainikka
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- cm
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software inconsistency error.
some interactions seem to be assigned multiple times.
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- vainikka
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Your system is blowing up. Does your university have a file sharing platform? If yes, upload your .top .itp and system .gro files there and put a link here.
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- cm
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If i again, on the constrain the md simulation is not happening.
These are the following steps to prepare the system
1.minimized protein in vaccujm
2. solvate the box
3. added ions and sugar itp in the top file.
Even if i, put only two sugar, minimization is not happenng, if the constrain is on.
Is there any other method, in which i can add sugar so that i can prepare the system.
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- vainikka
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- cm
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If i use -nt 12 option, then simulation is running well for only glucose but the problem is when i am choosing number of glucose upto about 50.
But when i am choosing trehalose, the minimization is running well with the help of -nt 12. But about almost about 10 trehalose. The equilibration is stopped by the segmentation fault. Why for the trehalose this is happening, because i am following the same procedure and mdp, itp file.
My question is,
i want to maintain the concentration of trehalose/GLUCOSE 1(M), should i follow the same procedure to calculate the number the of sugar in the water box. Because in case of cg, all the water and sugar molecules are in bead form.
The box length is 11.24 nm (cubic).
I have not change the itp file of sugar, just downloaded from this website.
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