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[modeller_usage] Re: SO4 ion coordinates not written

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: 
    Ph.: 713-500-6126
    Fax: 713-500-0652

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