[AMBER] Calcium parameters in calmodulin

From: bharat lakhani <lakhbharat.gmail.com>
Date: Thu, 13 Nov 2014 11:16:59 -0500

Hello All,

I've gotten AMBER program to recognize Ca2+ ions in the structure
coordinated with ASP (OD2 atomtype), but when I keep the CONNECT
information in the bottom of the PDB file, which tells the program how to
connect the Ca2+ to ASP residues, the program doesn't know or can't find
the bond and angle parameters for the bonds between the Ca2+ and oxygens
from the residues (since frocefield does not have the parameters for the
ca2+). Because of this, I cannot make .inpcrd or .prmtop files and so
cannot run the simulation.

I notice that if I take the CONNECT data out, I can form the .inpcrd and
.prmtop files just fine---but I don't want to do that because then I assume
the Ca2+ are simply floating around, and they need to be a part of the
calmodulin structure because they are what determine its active for, so i
am puzzling over it? Any suggestion on this would be great help
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Received on Thu Nov 13 2014 - 08:30:02 PST
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