normal Tutorial on Sugars

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10 years 4 months ago #3492 by robrob2013
Tutorial on Sugars was created by robrob2013
Hi I am planning to simulate a lipid bilayer covered by MALTOHEPTAOSE (AMylose)

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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10 years 4 months ago - 10 years 4 months ago #3493 by Clement
Replied by Clement on topic Tutorial on Sugars
Hi Rob,

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!
Last edit: 10 years 4 months ago by Clement.

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10 years 4 months ago #3498 by siewert
Replied by siewert on topic Tutorial on Sugars
Maltose is present in the itp file, so that couldn't be the problem.

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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3 years 6 months ago #8770 by sruthip
Replied by sruthip on topic Tutorial on Sugars
I have been trying to simulate a system with coarse-grained maltoheptose. I do not get any errors during energy minimization. But, during nvt equilibration I get the following error " The sum of two largest charge group radii (11.34) is larger than rlist".

Where am I going wrong? Please suggest.

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3 years 4 months ago #8846 by cm
Replied by cm on topic Tutorial on Sugars
can you please suggest me how to do coarse grained structure of trehalose. The itp file is already present. I have downloaded the pdb. Now i want to add 2(M) solution of trehalose (coarse grained structure) in the aqueous solution.

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3 years 4 months ago #8847 by vainikka
Replied by vainikka on topic Tutorial on Sugars
cm,

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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3 years 4 months ago #8848 by cm
Replied by cm on topic Tutorial on Sugars
Thank you so much..for your reply regarding the gmx insert option.

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3 years 4 months ago - 3 years 4 months ago #8852 by cm
Replied by cm on topic Tutorial on Sugars
can you please guide me, if it is possible to convert all tom pdb to coarse grained pdb of trehalose by using martinize.py script. The all atom .pdb of trehalose has been downloaded from the pubchem. When ever i am trying to convert the all atom pdb to coarse grained pdb by using martinize.py script, i am not geting the bead structure. Please suggest me the possible wayout.
I am now able to insert the all atom pdb of trehalose in the coarse grained water box.
Last edit: 3 years 4 months ago by cm.

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3 years 4 months ago #8853 by vainikka
Replied by vainikka on topic Tutorial on Sugars
You had the CG itp file, right? Then you don't need martinize, just put the right amount of beads in a box (you can for example take a lipid .gro file and remove some beads until you get the right amount) and minimize.

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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3 years 4 months ago - 3 years 4 months ago #8855 by cm
Replied by cm on topic Tutorial on Sugars
I am trying to minimize the system according to your suggestion. But every time i am facing the bellow problem:
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.
Last edit: 3 years 4 months ago by cm.

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3 years 4 months ago #8857 by vainikka
Replied by vainikka on topic Tutorial on Sugars
How many beads do you have? Trehalose is 6 beads, yet your error message says 86 atoms.

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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3 years 4 months ago #8858 by cm
Replied by cm on topic Tutorial on Sugars
this has been done by using -maxwarn 1:
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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3 years 4 months ago #8859 by vainikka
Replied by vainikka on topic Tutorial on Sugars
Comments are preceded by ';'
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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3 years 3 months ago - 3 years 3 months ago #8860 by cm
Replied by cm on topic Tutorial on Sugars
i have tried according to your suggestion. it is working.
Does it will make any problem in further simulation, as i have remove the constrain.
Last edit: 3 years 3 months ago by cm.

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3 years 3 months ago #8861 by vainikka
Replied by vainikka on topic Tutorial on Sugars
In all likelyhood the bonds are in the itp file for minimization (and equilibration) purposes, so after you have a stable system you can turn the constraints on again. Remember to comment out the bonds when you turn the constraints on again.

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3 years 3 months ago - 3 years 3 months ago #8862 by cm
Replied by cm on topic Tutorial on Sugars
But during the equilibration time i am getting this error:
software inconsistency error.
some interactions seem to be assigned multiple times.
Last edit: 3 years 3 months ago by cm.

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3 years 3 months ago #8866 by vainikka
Replied by vainikka on topic Tutorial on Sugars
www.gromacs.org/Documentation/Errors?hig...igned_multiple_times

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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3 years 3 months ago #8880 by cm
Replied by cm on topic Tutorial on Sugars
sorry for replying late. I was trying to overcome the error.my university does not have any platform at all.
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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3 years 3 months ago #8881 by vainikka
Replied by vainikka on topic Tutorial on Sugars
Copy-paste the sugar itp file here, and the coordinates of a SINGLE sugar.

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3 years 3 months ago #8883 by cm
Replied by cm on topic Tutorial on Sugars
Thank you so much for your continuous suggestion and help.
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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