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Modified aminoacid residue topology
- lianaliana
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13 years 2 weeks ago #629
by lianaliana
Modified aminoacid residue topology was created by lianaliana
I have already read Marrink et al, J. Phys. Chem. B., 2007, concerning CG particle type selection, but I still haven`t found a way to build a topology for my modified residue. It has an additional COOH in its side chain. How can I build this "new" residue to use with Martini?
Thank you in advance.
Liana.
Thank you in advance.
Liana.
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- xavier
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13 years 2 weeks ago #631
by xavier
You should have a look at the Monticelli et al JCTC-2008 for the description of the amino acid side chain and their parameterization. The best is that you find some experimental data on partitioning of your new side chain (or run some atomistic simulations) to parameterize your model.
XAvier.
Replied by xavier on topic Modified aminoacid residue topology
lianaliana wrote: I have already read Marrink et al, J. Phys. Chem. B., 2007, concerning CG particle type selection, but I still haven`t found a way to build a topology for my modified residue. It has an additional COOH in its side chain. How can I build this "new" residue to use with Martini?
Thank you in advance.
Liana.
You should have a look at the Monticelli et al JCTC-2008 for the description of the amino acid side chain and their parameterization. The best is that you find some experimental data on partitioning of your new side chain (or run some atomistic simulations) to parameterize your model.
XAvier.
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