Hello,
I'm trying to run the PB calculations within mm-pbsa through the
DELPHI software version 4.0. To get the delphi.crg and delphi.siz
files, I copied the my_amber94_delphi.crg and my_parse_delphi.siz
files from the mm-pbsa tutorial. However, my big problem is the
charges for DNA residues. To get them I used tleap to generate a mol2
file describing my system and then added the recorded charges to the
delphi.crg file. I'm getting very big values in the binding energies
compared to either GBTOT or PBTOT as implemented in amber. I think
I'm missing some thing with the charges here since the big difference
is in the polar term of the solvation energy. I'm using amber 10 with
99SB ff.
Any help is so much appreciated.
Best Regards,
Khaled
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Received on Sat Dec 04 2010 - 17:30:02 PST
