Hi Justin-- > > I have a question about the alpha-aminoisobutyric acid (AIB) residue in > protein-3.2.top. Does the force field need an additional improper to enforce > CA chirality? Aping from the Glycine residue, something like > > improper CB1 CB2 N C > > I would like for CB2 to be proS and CA1 to be proR, for consistency with other > amino acids. If I use the attached script to make AIB-AIB-AIB (pdb and psf > also attached) I find for residue 1 CB1 is proR and for residues 2 and 3 > CB2 is proR. I guess it chooses at random? >
Right. The topology entry is incomplete without the improper you mention above. However, you also need to add the corresponding parameter lines: improper CT CT NH1 C $kchi 0 69.0 ! AIB improper CT CT NH3 C $kchi 0 69.0 ! AIB Then the stereochemistry will be well-defined. If this definition fits what you'd like, please let me know and I'll add these entries to the default distributed Xplor-NIH values. Otherwise, try flipping the sign of the improper. But please let me know which you choose. > The comments in the topology file mention that phi/psi are not restrained > by dihedrals. I understand why, in general, this is the proper strategy. I > believe I have a case where I can make diastereospecific assignment of AIB > methyls from the data, though. I would like to enforce a phi angle > restraint. For phi/psi you could use dihedral restraints. You might also enable the 1-4 nonbonded term. thanks-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
