normal Capping CG proteins

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8 years 8 months ago #908 by OJA_DK
Capping CG proteins was created by OJA_DK
Hi.

I am currently running simulations on a domain of a larger protein. As the sequence of the domain sits in the middle of the full length protein sequence, it should not be given charged backbone beads. However, the martinize script automatically gives the terminal backbone beads a charged bead type. I am wondering whether I should just remove the charge and maintain the bead type, or if both the charge and the bead type should be changed.

I would like to know what your take on this is.

Best regards
Ole

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8 years 8 months ago #909 by xavier
Replied by xavier on topic Capping CG proteins
Dear Ole,

You should definitely remove the charge and possibly change the bead type. The Q type are very hydrophilic. It could be an idea to reduce the interaction level by defining the bead as a N0 bead type.

Note however that I the system was separated from the rest it would naturally be charged and polar in physiological conditions!

OJA_DK wrote: Hi.

I am currently running simulations on a domain of a larger protein. As the sequence of the domain sits in the middle of the full length protein sequence, it should not be given charged backbone beads. However, the martinize script automatically gives the terminal backbone beads a charged bead type. I am wondering whether I should just remove the charge and maintain the bead type, or if both the charge and the bead type should be changed.

I would like to know what your take on this is.

Best regards
Ole

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8 years 8 months ago #910 by OJA_DK
Replied by OJA_DK on topic Capping CG proteins
Dear Xavier.

It is a good point that the terminals will be charged if the domain is seperated from the rest of the protein under physiological conditions.

We have access to experimental data for both the full length protein and for the isolated domain. Until now I have been running simulations with charged terminals, so the simulations should represent the isolated domain. Here I saw a clear interaction between a positively charged residue and the C-terminal. Now I would like to try to run them without charged terminals to see how big a difference it makes on the system.

I will try removing the charge, and change the bead types to N0.

I thank you for your reply.

Best regards
Ole

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