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protein-membrane (POPG) interaction
- busato
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9 years 1 month ago #4475
by busato
protein-membrane (POPG) interaction was created by busato
Dear User,
I am a new user of Martini ff, I simulated the interaction between a protein and membrane.
First, I am interested to know which aminoacids are involved in the interaction with the membrane along my trajectory. (for example which aa are within of 0.6 nm from the surface of the membrane).
Are there any scripts or tools to perform this kind of analysis?
Second, I would like to know the limit of distance of a acceptable salt bridge interaction in Martini ff.
I really appreciate your help.
Thank you,
Mirko
I am a new user of Martini ff, I simulated the interaction between a protein and membrane.
First, I am interested to know which aminoacids are involved in the interaction with the membrane along my trajectory. (for example which aa are within of 0.6 nm from the surface of the membrane).
Are there any scripts or tools to perform this kind of analysis?
Second, I would like to know the limit of distance of a acceptable salt bridge interaction in Martini ff.
I really appreciate your help.
Thank you,
Mirko
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- Clement
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9 years 1 month ago #4476
by Clement
Replied by Clement on topic protein-membrane (POPG) interaction
Welcome Mirko!I am a new user of Martini ff, I simulated the interaction between a protein and membrane.
I'd check g_select, included in the Gromacs package. Syntax very comprehensible.First, I am interested to know which aminoacids are involved in the interaction with the membrane along my trajectory. (for example which aa are within of 0.6 nm from the surface of the membrane).
Are there any scripts or tools to perform this kind of analysis?
For that one... If by salt bridge you mean hydrogen bonding, remember you're dealing with CG here, and not such things exist... What do you want to check/quantify/measure exactly?Second, I would like to know the limit of distance of a acceptable salt bridge interaction in Martini ff.
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- busato
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9 years 1 month ago #4477
by busato
Replied by busato on topic protein-membrane (POPG) interaction
Thank you for your reply,
Yes I checked g_selected and I also found a command g_mindist.
Yes, you are right, Infact now I have performed a map of contact between protein (aa) and membrane (cutoff 0.4 nm).
1)I would like to find a way to quantify and understand the possible interactions and the type of interaction.
2)What interactions can I study in Martini ff? and What rules these interactions have to follow (distances, angles ..)?
Thank you very much,
Mirko
Yes I checked g_selected and I also found a command g_mindist.
Yes, you are right, Infact now I have performed a map of contact between protein (aa) and membrane (cutoff 0.4 nm).
1)I would like to find a way to quantify and understand the possible interactions and the type of interaction.
2)What interactions can I study in Martini ff? and What rules these interactions have to follow (distances, angles ..)?
Thank you very much,
Mirko
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- Clement
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9 years 1 month ago - 9 years 1 month ago #4478
by Clement
EDIT: I guess you want to check things in a similar way as hydrogen bonds or something. Directivity, distance, angle, ... defining if interaction there is. I think you have to define your proper rules in Martini if you really need them. But remember you're dealing with a CG FF, and interactions loose most of their directivity as compared to AA simulations. You have to rethink the way of analyzing things, but it's more a simplification.
Replied by Clement on topic protein-membrane (POPG) interaction
0.4 nm seems a bit too short to me... Remember Martini beads have an effective radius of 0.47 nm in average. I'd increase your cutoff to 0.7 nm at least, if not slightly more.[...] map of contact between protein (aa) and membrane (cutoff 0.4 nm).
Well... There I'd need more information about what you mean by that. Martini defined non-bonded interactions are van der Waals and electrostatic, but hydrophobic interactions can be observed equally. What do you want to analyze exactly?[...] quantify and understand the possible interactions and the type of interaction.
There again I need more precisions. Isn't this question a bit similar to your previous one? At least I understand it this way.What interactions can I study in Martini ff? and What rules these interactions have to follow (distances, angles ..)?
EDIT: I guess you want to check things in a similar way as hydrogen bonds or something. Directivity, distance, angle, ... defining if interaction there is. I think you have to define your proper rules in Martini if you really need them. But remember you're dealing with a CG FF, and interactions loose most of their directivity as compared to AA simulations. You have to rethink the way of analyzing things, but it's more a simplification.
Last edit: 9 years 1 month ago by Clement.
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- busato
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8 years 11 months ago #4529
by busato
Replied by busato on topic protein-membrane (POPG) interaction
Thank you very much,
I used in my analysis 0.7 nm (cut-off for the distance between protein and membrane) as you suggested me.
Can you suggest me some papers which I can find and read in detail about the Martini beads have an effective radius of 0.47 nm in average?
Thank you very much,
Mirko
I used in my analysis 0.7 nm (cut-off for the distance between protein and membrane) as you suggested me.
Can you suggest me some papers which I can find and read in detail about the Martini beads have an effective radius of 0.47 nm in average?
Thank you very much,
Mirko
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- helgi
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8 years 11 months ago #4530
by helgi
Replied by helgi on topic protein-membrane (POPG) interaction
An effective radius of a MD bead/atom comes from it's van der waals interactions with other beads. The pick of 0.47 nm for Martini is discussed in the original Martini papers:
S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. The MARTINI forcefield: coarse grained model for biomolecular simulations. JPC-B, 111:7812-7824, 2007.
S.J. Marrink, A.H. de Vries, A.E. Mark. Coarse grained model for semi-quantitative lipid simulations. JPC-B, 108:750-760, 2004
Cheers,
- Helgi
S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. The MARTINI forcefield: coarse grained model for biomolecular simulations. JPC-B, 111:7812-7824, 2007.
S.J. Marrink, A.H. de Vries, A.E. Mark. Coarse grained model for semi-quantitative lipid simulations. JPC-B, 108:750-760, 2004
Cheers,
- Helgi
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