normal Peptide sidechains rotate more than 180 degrees

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10 years 8 months ago #2795 by nanogod
Hey guys,

I have a problem with some peptides in water as some of the amino acid sidechains rotate more than 180 degrees during my md run! This means that two neighbour amino acids end up with the sidechain parallel and very closeto eachother. How can I prevent this in a no too intrusive way?

the following md parameters:
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 90

Kind regards
Nanogod

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10 years 8 months ago #2897 by xavier
Hi,

You mean you are looking at unstructured peptide in solution? This is indeed a problem of lacking a directionality of the side chains one relative to the other. This is not a problem for structured proteins.

We have fixed this problem in a few studies by adding a dihedral angle to impose the opposite direction of two consecutive side chains.

It should be quite easy to set it up.

nanogod wrote: Hey guys,

I have a problem with some peptides in water as some of the amino acid sidechains rotate more than 180 degrees during my md run! This means that two neighbour amino acids end up with the sidechain parallel and very closeto eachother. How can I prevent this in a no too intrusive way?

the following md parameters:
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 90

Kind regards
Nanogod

Please Log in or Create an account to join the conversation.

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