Dear Charles and other Xplorers, I have two basic questions about calculations which I would like to set up.
1. I have an X-ray structure to which I would like to add a derivatized amino acid (ie: MTSL) for which I have the topology and parameter files. I know how to create an extended structure incorporating this residue but so far have not figured out how I can read in the crystal coordinates, substitute coordinates for this residue only and write out a new coordinate file maintaining the accuracy of the crystal structure. 2. I want to then use that derivatized structure to perform a rigid-body minimization of this two-domain protein based on RDC data and inter-domain long-range paramagnetic restraints to the derivatized residue, again without changing the crystal coordinates of the two domains. I had a look in the "prot-prot" example in "eginputs" and will start from there. Since I can specify which residues have torsion angle freedom (in our case the linker only) will this protocol be sufficient for maintaining the accuracy of the crystal structure? I would really appreciate any help with these questions to help me in starting off in the right direction with this project.
