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11 years 1 month ago #1459 by Rajat Desikan
Is it possible to calculate salt bridges in Martini? was created by Rajat Desikan
Hi All,
I have a fully atomistic as well as a Martini simulation of a protein in membrane. I want to calculate the number of salt bridges using standard gromacs tools (g_saltbr) and compare the numbers I get in the two simulations. Is this feasible? Are there any pitfalls that I should be aware of? The protein is highly negatively charged (-60), therefore I have 60 Na+ ions in both simulations.

Thanks

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11 years 1 month ago #1460 by xavier
Replied by xavier on topic Is it possible to calculate salt bridges in Martini?
Yes g_saltbr would work with a MARTINI protein. However as you mention a membrane protein you should be aware that the program will also count the lipids head groups as charged groups and look and the interactions ... removing the lipids from the trajectory and tpr might be a good idea.

Rajat Desikan wrote: Hi All,
I have a fully atomistic as well as a Martini simulation of a protein in membrane. I want to calculate the number of salt bridges using standard gromacs tools (g_saltbr) and compare the numbers I get in the two simulations. Is this feasible? Are there any pitfalls that I should be aware of? The protein is highly negatively charged (-60), therefore I have 60 Na+ ions in both simulations.

Thanks

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11 years 1 month ago #1461 by Rajat Desikan
Replied by Rajat Desikan on topic Is it possible to calculate salt bridges in Martini?
Thanks a lot, Xavier.
I know how to remove the lipids from the trajectory file. But how do I remove it from the .tpr?

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11 years 1 month ago #1469 by Rajat Desikan
Replied by Rajat Desikan on topic Is it possible to calculate salt bridges in Martini?
Hi All,
I have a query regarding the distance cutoff for saltbridges in Martini.

For the fully atomistic simulation, I analysed saltbridges in VMD using a distance cutoff of 3.2 ang (Between oxygen and nitrogen atoms of opposite charged AA) and got around 12 saltbridges. However, for the Martini simulation, the same distance cutoff yields zero salt bridges (no output until a cutoff of 5 ang). Is there a need for a bigger cut-off?

Thanks

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11 years 1 month ago #1470 by xavier
Replied by xavier on topic Is it possible to calculate salt bridges in Martini?
To remove the lipids from the tpr you can either use the tpbconv command giving an index and select a group where the lipid have been removed .... the output tr will then not contain the lipids. This might work.

If not you can generate a new tpr be simply defining a system without lipids and use that new tpr.

Rajat Desikan wrote: Thanks a lot, Xavier.
I know how to remove the lipids from the trajectory file. But how do I remove it from the .tpr?

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11 years 1 month ago #1471 by xavier
Replied by xavier on topic Is it possible to calculate salt bridges in Martini?
The minimum distance between two beads in Martini is 5.2 Ang/0.52 nm so you will not observe any salt-bridge at 3.2 ang. You have to increase the cut-off ... 0.6/0.7 nm should be fine.

The best way to choose the cutoff is to choose a salt bridge you know is present (eg. by visualisation) and plot the histogram of the distance ... the minimum after the first pic should be your cutoff.

Rajat Desikan wrote: Hi All,
I have a query regarding the distance cutoff for saltbridges in Martini.

For the fully atomistic simulation, I analysed saltbridges in VMD using a distance cutoff of 3.2 ang (Between oxygen and nitrogen atoms of opposite charged AA) and got around 12 saltbridges. However, for the Martini simulation, the same distance cutoff yields zero salt bridges (no output until a cutoff of 5 ang). Is there a need for a bigger cut-off?

Thanks

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11 years 1 month ago #1472 by Rajat Desikan
Replied by Rajat Desikan on topic Is it possible to calculate salt bridges in Martini?
Hi Xavier,
That is a wonderful piece of advice. Thanks.

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11 years 1 month ago #1473 by Rajat Desikan
Replied by Rajat Desikan on topic Is it possible to calculate salt bridges in Martini?
I calculate the histogram of the distance between the residues participating in the salt bridge using g_mindist, right? Or is there a better way?

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11 years 1 month ago #1474 by xavier
Replied by xavier on topic Is it possible to calculate salt bridges in Martini?
G_mindist, g_dist, vmd, any tool would do the distance, the distribution you have to make yourself ... some gmx tools do it for you though. If not xmgrace or excel should do.

Rajat Desikan wrote: I calculate the histogram of the distance between the residues participating in the salt bridge using g_mindist, right? Or is there a better way?

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