ADL: pdbqs

Filippo Marchioni Filippo.Marchioni at cchmc.org
Tue Apr 3 10:12:27 PDT 2007


Hi all,
I have a quick question about the pdbqs file.
It contains the coordiante x,y,z, of the atoms; the charge and the
solvatation parameter. 

After the coordinates  there are actually two columns one that is
usually present also in the pdb file, I though was a dummy charge column
that assigne 1 to all the atoms, and another one that, together with the
three columns for solvatation's parameters, is created during the
writing of the pdbqs. 
Are this suppositions correct? 
If they are why also in the tutorial example this second column report
value that aparently don;t make any sense? 

I my specific case I have a protein containing Mg and in the pdb file
the 
assigned charge is 1 and in the pdbqs is 8.43. 
Does anybody experience the same? 

Thanks in advance for any help that will be very appreciated

Best
Filippo
 



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