normal protein-CG

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13 years 8 months ago #390 by smitha
protein-CG was created by smitha
I have a doubt regarding the CG for proteins (in my case peptide) . We have generated the local minimum conformations for a peptide with the given sequence and it is all atom based . I would like to do the CG model for the same . I came to know about the martini force field . I would like to apply the same . I have gone through the tutorial . I have tried in generating the initial CG file for the all atom file . I would like to know how the energy is calculated for a conformation . where is the program or one has to go with some other program . I saw only parameter generation file and it will be also helpful to me if i know the solvation and the energy of the total system .

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13 years 7 months ago #396 by xavier
Replied by xavier on topic protein-CG
The best for you would be to read the Martini paper on the extension to proteins. This would give you a precise idea of the different energy terms used to calculate the potential energy of the system.

Then the calculation itself is done most often through gromacs. You have to generate a topology and use the mdrun program to obtain an energy value for a conformation. Going through the various tutorials available on the web site would certainly help you in getting what you want.

XAvier.

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