I am using Rosettascripts (version 3.5) to redesign the protein-protein interface, I use the following applications to redesign the interface,
1. Minmover - for energy minimization
2. PackrotamersMovers - for repacking and redesigning of interface residues
3. set of filters to filter the output
I would like to apply some restrictions on the amino acid selection during the redesing process which are,
1. retain the native ALA amino acids while redesigning and
2. do not substitute ALA aa while redesinging
I used a resfile for this with "* A NOTAA G", this removed all the native ala residues and also didt consider the ala for substituion. But I want to retain the native ala residues at the same time not substituting a amino acid with ala residue. Can someone give me a solution for this?
Thanks in advance for your suggestions.