Dear Amberists,I am trying to simulate a protein that binds to adenosine triphophaste (ADP), phosphoenol pyruvate (PEP), potassium (K) and two magnesium (Mg) atoms.
For potassium I used the ions from frcmod.ionsjc_tip4pew.ADP and magnesium were taken from
http://www.pharmacy.manchester.ac.uk/bryce/amber/PEP I parametrized using G03 as described here (RESP calculation)
http://www.teokem.lu.se/~ulf/Methods/resp.html This step as well as subsequent runs in antechamber and parmchk2 finish without error.
When the protein used in the simulation is in a open state. i.e. ligands are not constrained by the protein itself, everything goes well. But, when I use a protein in the closed state, where the ligands are constraint together, the phosphate that is part of the phosphoenolpyruvate is deformed. That is, the oxigens bound to the phosphor seem to be pushed together. This happens only for the phosphate in PEP but not for those in ADP. When I run simulations with PEP and ADP only, the phosphate group looks ok. When I start adding K or Mg, PEP gets deformed but far less than in the pentacomplex. I interpret this as if my parametrization is incorrect or flawed.So, I ask two questions:Is there an obvious mistake I am making while trying to parametrize and simulate this complex? My input file for leap loads alf the frcmod and in or prep files without showing any error. The atom and fragment files are named correctly, as far as I can tell.Maybe this kind of complex substrate will be better prepared via MCPB?I'll add l
inks to both my input for tleap as well as for the leap.log below. Thanks in advance.
https://dl.dropboxusercontent.com/u/10280828/leap.log
https://dl.dropboxusercontent.com/u/10280828/tleap-1A49FH_A_PEP_K_2Mg_ADP.in
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Received on Fri May 15 2015 - 13:00:02 PDT
