how to use rosettadesign to do mutations on protein structure

[Anonymous]

Dear all:

I am learning to use rosettadesign to do mutations on protein structure. I do not know how to prepare the resfile. In my protein, I only need to do two mutations, for examle, V42M and M24V. In such kind of case , how the resfile looks like?

I prepared one like following:

ALLAA
start
24 A NOTAA V
42 B NOTAA M

could that make sense? Thanks a lot.

[Anonymous]

The resfile format looks fine( it should not all be on one line but that looks like a web formatting error ). Is the problem that you are getting mutations at positions 24 and 42 but they are not the desired mutations? If so try

ALLAA

start

24 A PIKAA M

43 B PIKAA V

Grant

[bpierce]

> Dear all:
>
> I am learning to use rosettadesign to do mutations on protein structure. I do not know how to prepare the resfile. In my protein, I only need to do two mutations, for examle, V42M and M24V. In such kind of case , how the resfile looks like?
>
> I prepared one like following:
>
> ALLAA
> start
> 24 A NOTAA V
> 42 B NOTAA M
>
> could that make sense? Thanks a lot.
>
>

[bpierce]

Actually, if you only want to make a double mutant, this is what you want in your resfile:

NATAA

start

24 A PIKAA M

43 B PIKAA V

The default NATAA will allow non-mutated residues to repack around your mutations, whereas the default ALLAA would have caused all residues everywhere to be designed, resulting in many mutations (not just the 2 you want).

Also, are you working on a dimer? If not, you probably don’t want 2 different chain IDs (A & in your resfile. If it’s a dimer and the mutations are on different subunits, you are fine. Also, just a little tip. You might want to specify NATRO as the default, and then use NATAA only for specific residues near your mutations (I get better results that way).

V.
> Dear all:
>
> I am learning to use rosettadesign to do mutations on protein structure. I do not know how to prepare the resfile. In my protein, I only need to do two mutations, for examle, V42M and M24V. In such kind of case , how the resfile looks like?
>
> I prepared one like following:
>
> ALLAA
> start
> 24 A NOTAA V
> 42 B NOTAA M
>
> could that make sense? Thanks a lot.
>
>

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