Re: [modeller_usage] Re: SO4 ion coordinates not written

[Modeller Caretaker <>]

Cheri M Turman wrote:
> 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??

SO4 is not exactly 'defined' in the restyp.lib file; as you noticed, its 
code is '#' (which usually means 'undefined' in Modeller). By default, 
Modeller will probably use top_heav.lib and par.lib, although these are 
derived from the CHARMM files you looked at, and thus don't have SO4 
parameters or topology.

> 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.

That's correct. You will need to add the topology and parameters for SO4 
if you want it to be treated as non-rigid (there's a FAQ for this).

	Ben Webb, Modeller Caretaker
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