Hello --

Can you please attach all of your *.pqr files and *.in files so we can debug this more easily?

Thanks,

Nathan

2008/11/27 <d.c.guo@smail.hust.edu.cn>
Hi All,
It's my first time using APBS. Iam trying to calculate thebinding energy for protein complex(aa0007.pdb.pqr) that consists of aa0007_l..pdb.pqr + aa0007_r.pdb.pqr

1. can this .in file calculate the binding energy includesolvation contributions and coulombic contributions?

2. Whether the result 100KJ/mol is better for binding than 50KJ/mol or not?

my .in file:

read
mol pqr aa0007.pdb.pqr
mol pqr aa0007_l.pdb.pqr
mol pqr aa0007_r.pdb.pqr
end
elec name com_water
mg-auto
dime 129 129 161
cglen 67.1730022431 91.7640008927 160.236001968
cgcent mol 1
fglen 44.7820014954 61.1760005951 106.824001312
fgcent mol 1
mol 1
lpbe
bcfl sdh< br /> pdie 2.0000
sdie 78.5400
srfm smol
chgm spl2
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
calcenergy total
calcforce no
end
elec name lig_water
mg-auto
dime 129 129 161
cglen 37.1115002633 46.1235008239 160.236001968
cgcent mol 1
fglen 24.7410001755 30.7490005493 106.824001312
fgcent mol 1
mol 2
lpbe
bcfl sdh
pdie 2.0000
sdie 78.5400
srfm smol
chgm spl2
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
calcenergy total
calcforce no
end
elec name rec_water
mg-auto
dime 129 129 161
cglen 67.1730022431 91.7640008927 160.236001968
cgcent mol 1
fglen 44.7820014954 61.1760005951 106.824001312
fgcent mol 1
mol 3
lpbe
bcfl sdh
pdie 2.0000
sdie 78.5400
srfm smol
chgm spl2
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
calcenergy total
calcforce no
end
print energy com_water - lig_water - rec_water end
quit

Thanks in advance


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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/