In my inhibitor-protein complex, there is a MN ion. I used the following command to run per-residue free energy decomposition with MMPBSA.py in AmberTools 12.
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp com_solv.prmtop -cp com_nosolv.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
Here is the input file:
Per-residue GB and PB decomposition
&general
startframe=3500, verbose=1, search_path=1,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
dec_verbose=3,
/
The program aborted with the following error:
Beginning GB calculations with /home/Amber/amber11/exe/sander
calculating complex contribution...
CalcError: /home/Amber/amber11/exe/sander failed with prmtop A-WFE-nw-nc.prmtop!
When the MN ion was replced by a MG ion, no such error was found in the output file.
It seems that the parameter of MN should be added to the file mdread.f in AMBERHOME/src/sander. Does anyone know how to get the relative parameter of MN?
Or could I use the one of Fe instead?
Thanks!
Cao Yang
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Received on Tue Jun 19 2012 - 07:30:02 PDT
