Hi all,
I am trying to refine a protein complex structure using Xplor-NIH that has already been calculated using CYANA. Here this complex consists of the first chain as protein and second chain as a peptide which is having modified residues (phosphorylated Thr: TPO, phosphorylated Ser: SEP, acetylated N-term: ACE and amidated C-term: CTN). As I understood correctly by looking at the topology file, Xplor-NIH patches the phosphate group onto already existing residues in order to change into the phosphorylated residue. This works well when you are starting the structure calculation. Now I am wondering about the refinement of an existing structure that already has modified residues in it. I have the following questions regarding the Xplor-NIH refinement of this system: 1. For refinement, should I need to incorporate the modified residues (define new residues i.e. TPO, SEP similar to ACE) in the topology file (protein-1.0.top)? or change these residues in my input files to conventional residues and at the end put the phosphate group (I mean use the same method as calculating the structure). 2. If I am going to define these residues, how one would calculate the charge and masses associated with additional atoms. Much appreciation in advance for any help! -- Best Regards, Karuna Dixit Postdoctoral Research Associate Department of Biochemistry & Biophysics Texas A&M University Email: [email protected] ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
