On Thu, 2014-11-13 at 11:16 -0500, bharat lakhani wrote:
> 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
You need to supply these bond, angle, and dihedral parameters to tleap.
These parameters do not exist in the standard Amber force fields, so you
need to determine them yourself.
A program like MCPB (metal center parameter builder) can help here.
Note that what you are trying to do is a lot harder than just adding
calcium ions to a simulation, since it is not trivial to derive the
parameters you are looking for.
Furthermore, the standard ASP and Ca2+ charges will not be the same in a
bonded model vs. a non-bonded model, so you will probably need to derive
charges for your new residue as well.
I encourage you to look into MCPB and the related literature (the MTK++
manual in $AMBERHOME/AmberTools/src/mtkpp/doc is a good starting place).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 13 2014 - 09:00:03 PST
