Hello Russell-- > I am writing to request advice on how best to patch unusual chemical moieties > to > the termini of peptide sequences. For simplicity, I would like to define > the > moiety as a special type of amino acid and then use a toph.pep file to > generate > the sequence. > > -Russell > > Hello Russell-- > > Are genCircPep.py or genModCircPep.py in the eginput/PSF_generation > subdirectory of the Xplor-NIH distribution useful in this regard? If > not, I can probably dig up some other examples. > > best regards-- > Charles > > I have been able to move forward and construct a few cyclic beta > peptide foldamers (like ACPC-8) that have qualitatively correct > geometries. As I attempt to finish up, I have run across two > problems that might be of general interest. > > Firstly, I receive interatomic distance and angle error messages > when running a sa_accept.inp script on the SA geometries. I believe > this is because the carbon and hydrogen atoms in each building block > are confined to a 5-membered ring. I have used only “CT” type > carbons in the building blocks. Is it best to use another carbon > type (such as “CP”) in the ring to minimize these errors or are the > errors just an artefact and the final SA geometries the same > regardless of carbon type?
If you have a nonstandard amino acid, it is normal to introduce new atom types such that unique type-based parameters can be introduced. > > Also, I enforce a trans geometry between the HA/HB atoms of each > building block by defining an improper dihedral --HA CA CB HB-- that > I set to a value derived from the X-ray structure. I am very > sceptical about this! This improper may be the source of the > problems above. Can anyone suggest a better way to maintain a trans > geometry between the HA/HB and NH/CO moieties in cyclic beta > peptides such as ACPC? You can use the DIHE term for this. As IMPR is identical, that might also be an acceptable solution. I'm happy to assist you with further details on getting the correct parameters for this moiety. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
