Hi all,
My recent job is a MD simulation of a ligand-protein complex. The ligand is quercetin, a kind of flavonoids. I used GAFF for the ligand and ff99SB for the receptor. By examining the trajectories, I found that the ligand distort abnormally. What shoud I do to deal with this problem?
Maybe a proper force filed for the ligand is needed.
The following is the frcmod file created by parmchk.
remark goes here
MASS
BOND
ANGLE
DIHE
c -cd-oh-ho 1 1.050 180.000 2.000 same as X -c2-oh-X
cd-cc-os-ca 1 1.050 180.000 2.000 same as X -c2-os-X
cd-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
ho-oh-cd-cc 1 1.050 180.000 2.000 same as X -c2-oh-X
os-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
ca-os-cc-ca 1 1.050 180.000 2.000 same as X -c2-os-X
IMPROPER
ca-ca-ca-oh 1.1 180.0 2.0 Using default value
c -ca-ca-ca 1.1 180.0 2.0 Using default value
ca-cd-c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c -cc-cd-oh 1.1 180.0 2.0 Using default value
ca-cd-cc-os 1.1 180.0 2.0 Using default value
ca-ca-ca-os 1.1 180.0 2.0 Using default value
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-cc 1.1 180.0 2.0 Using default value
ca-ca-ca-o 1.1 180.0 2.0 Using default value
NONBON
Many thanks.
Mu Xia,
Zhejiang University, China
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Received on Wed Oct 17 2012 - 04:30:03 PDT
