Me again, Modeling SO4 explicitly may be more complicated than I thought...not sure? However, I looked into what I guess are the CHARMM topology (top_all22_prot_b5.inp) and parameter (par_all22_prot_b5.inp) files that MODELLER uses by default and there was no entry for SO4. This is puzzling since SO4 is defined in the retyp.lib file. Has anyone been successful with changing SO4 single letter PDB entry in the restyp.lib and having MODELLER use top and parms for it? If so, where are the top and parms for SO4 located? Maybe I just overlooked them??
Anyway, I was able to get the SO4s to work using 'BLK' notation with '.' in the .ali file. If I read correctly, this means that there is no topology or parameters associated with 'BLK' so they are modeled as rigid bodies based on the template structure coordinates. They appear fine in the output coordinates so I am happy to proceed with this process. But, I would still like to know if there are CHARMM top and parms for SO4 if anyone knows. Cheers, Cheri
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Cheri M. Turman Graduate Student University of Texas-Houston Medical School 6431 Fannin Houston, TX 77030 USA
e-mail: cheri.m.turman@uth.tmc.edu Ph.: 713-500-6126 Fax: 713-500-0652