Hello Adel-- > How are you. I am trying to do refinement using the eefx and I need > to add cis bond between residue 40 and 41, proline is the 41^st. In > my script I have the following > > # load PDB to generate PSF > > import glob > > protocol.loadPDB( glob.glob(inTemplate)[0], > > deleteUnknownAtoms=True, ) > > import psfGen > > psfGen.cisPeptide(resid=40) > > while the calculation ran, in some of the structure I am missing atoms between > the 40^th and 41^st residues. Also even in the structures that did not have > missing atoms, it seemed the protons on the 40^th glycine are linked together. > I would appreciate any help. Thank you so much. >
Oops- there were some missing cis-peptide parameters for EEFx. Please copy this file: https://nmr.cit.nih.gov/out/protein_eefx2.par to the toppar/eefx directory of your Xplor-NIH distribution. Do let me know if you have any problems. In particular, please look for the presence of the string "ERR" in the output file. best regards-- 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
