Dear All,
When I use ambertool to prepare the parameters of my ligand, I can get the
new.frcmod, however, I could not save the prmtop files. How shoul I do?
Thanks for your help!
It seems that gaff.dat does not contains such parameters, how to add them to
gaff.dat? The attached lig.pdb contains 4 Cl atom, two of which are in
pheonic ring and another two are in a single SP2 Carbon C.
The errors:
Building proper torsion parameters.
** No torsion terms for ca-ca-ce-c2
** No torsion terms for ca-ca-ce-c2
** No torsion terms for ca-ca-ce-ca
** No torsion terms for ca-ca-ce-c2
** No torsion terms for ca-ca-ce-ca
** No torsion terms for ca-ca-ce-c2
** No torsion terms for ca-ce-ca-ca
** No torsion terms for ca-ce-ca-ca
The content of frcmod:
remark goes here
MASS
BOND
ANGLE
DIHE
ca-ce-ca-ca 1 2.550 180.000 2.000 same as X
-c2-ca-X
ca-ca-ce-c2 1 6.650 180.000 2.000 same as X
-c2-ce-X
IMPROPER
ca-ca-ca-ce 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)
c2-ca-ce-ca 1.1 180.0 2.0 Using default
value
ce-cl-c2-cl 1.1 180.0 2.0 Using default
value
NONBON
Great thanks
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Received on Thu Aug 04 2011 - 09:30:03 PDT
