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Regarding mapping of resonance molecules
- satnamphysics
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10 years 4 months ago #3042
by satnamphysics
Regarding mapping of resonance molecules was created by satnamphysics
Dear All ,
I have to map a molecule( alpha-tocopherol) to martini coarse grained format . But that molecule have other structure also. I have problem how to map it.. Thanks in advance...
I have to map a molecule( alpha-tocopherol) to martini coarse grained format . But that molecule have other structure also. I have problem how to map it.. Thanks in advance...
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- siewert
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10 years 4 months ago #3065
by siewert
Replied by siewert on topic Regarding mapping of resonance molecules
The following publication might be helpful, it contains a Martini model for vitamin E:
Tuning Membrane Phase Separation Using Nonlipid Amphiphiles
Author(s): Muddana, Hari S.; Chiang, Homer H.; Butler, Peter J.
Source: BIOPHYSICAL JOURNAL Volume: 102 Issue: 3 Pages: 489-497 DOI: 10.1016/j.bpj.2011.12.033 Published: FEB 8 2012
Tuning Membrane Phase Separation Using Nonlipid Amphiphiles
Author(s): Muddana, Hari S.; Chiang, Homer H.; Butler, Peter J.
Source: BIOPHYSICAL JOURNAL Volume: 102 Issue: 3 Pages: 489-497 DOI: 10.1016/j.bpj.2011.12.033 Published: FEB 8 2012
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- satnamphysics
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10 years 4 months ago #3173
by satnamphysics
Replied by satnamphysics on topic Regarding mapping of resonance molecules
Hi siewert,
First I want to say thanks to you. I have mapped my molecule into coarse grained structure file successfully by using VMD. I got .top file from VMD also. Now I have to create topology(.itp) for that molecule. Kindly help me to create it or conversion of .top to .itp.
Thanks in advance..
First I want to say thanks to you. I have mapped my molecule into coarse grained structure file successfully by using VMD. I got .top file from VMD also. Now I have to create topology(.itp) for that molecule. Kindly help me to create it or conversion of .top to .itp.
Thanks in advance..
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10 years 4 months ago #3175
by siewert
Replied by siewert on topic Regarding mapping of resonance molecules
The itp you will have to create by hand - you can look at example itp files on the Download section to see how such a file should look like. The required parameters (particle types, definition of bonded parameters) you can base on the publication I referenced in my previous reply.
See also the Tutorial pages where we describe in detail how to create new topologies from scratch!
Good luck ..
See also the Tutorial pages where we describe in detail how to create new topologies from scratch!
Good luck ..
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- satnamphysics
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10 years 3 months ago #3223
by satnamphysics
Replied by satnamphysics on topic Regarding mapping of resonance molecules
Hi Siewert,
Now I am going to create topology for tocopherol. But in the FQA about topology it is written that we have to take bond length .47nm and and force constant is 1250KJ/mol nm^2 .
A standard force constant of K =25 kJ mol-1 with an equilibrium bond angle φ = 180^0. I have also checked topology of DPPC(which is downloaded from this site ) is all standard(180 or 120) values are use. But the angles of the atoms are different.I could not understand why I have to use these values only even my bond length is different . Please explain. Thanks in advance....
Now I am going to create topology for tocopherol. But in the FQA about topology it is written that we have to take bond length .47nm and and force constant is 1250KJ/mol nm^2 .
A standard force constant of K =25 kJ mol-1 with an equilibrium bond angle φ = 180^0. I have also checked topology of DPPC(which is downloaded from this site ) is all standard(180 or 120) values are use. But the angles of the atoms are different.I could not understand why I have to use these values only even my bond length is different . Please explain. Thanks in advance....
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