Charles and Guillermo,
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? 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. Prior to this I need to know which carbon in my Newman projections is CB1 and which is CB2. Thanks for your help. Justin ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
3AIB.tgz
Description: 3AIB.tgz
