Re: [gmx-users] mutational analyses: Cystine and indels

Hi List, Has anybody have something else to add to the Peter's comments? Basically, I'm still unsure about modeling deletions. Any help is appreciated. Em 30-05-2012 17:37, Peter C. Lai escreveu: You might be able to use MODELLER for generating the helix deletions since it is alignment-based. If

Re: [gmx-users] mutational analyses: Cystine and indels

Hi Peter, Thanks for helping. I might not have been clear. The cys mutation is in a different location of the indel. I'm particularly worried about how the molecular modelling programs will treat indels. Several things can happen upon deletion of an helix residue. In this context, just take the

Re: [gmx-users] mutational analyses: Cystine and indels

You might be able to use MODELLER for generating the helix deletions since it is alignment-based. If you use automodel.make(exit_stage=2) it will generate coordinates based on the specified sequence-spatial alignment but will stop there (otherwise it will try to run simulated annealing in vacuum).

[gmx-users] mutational analyses: Cystine and indels

Hi Gromacs list, I would like to study two different mutations in a protein molecule, perhaps using MD. One of them is a insert deletion and the other is a mutation to Cys beside an existing Cys. The problem is that most of the molecular modeling programs, including Rosetta, do not handle with