Dear AMber users,
I was trying to get the parameters for my covalently linked nerve agent to serine 203,
SUN.mol2, I run simple antechamber and parmcheck, but after loading them to leaps
I am getting parameters errors ..
inside my parmcheck file is:
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
c3-h4-c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
NONBON
after reading into leap ...
FATAL: Atom .R<SUN 203>.A<N 1> does not have a type.
FATAL: Atom .R<SUN 203>.A<CA 2> does not have a type.
FATAL: Atom .R<SUN 203>.A<CB 3> does not have a type.
FATAL: Atom .R<SUN 203>.A<OG 4> does not have a type.
FATAL: Atom .R<SUN 203>.A<C 5> does not have a type.
FATAL: Atom .R<SUN 203>.A<O 6> does not have a type.
FATAL: Atom .R<SUN 203>.A<O1 7> does not have a type.
FATAL: Atom .R<SUN 203>.A<P1 8> does not have a type.
FATAL: Atom .R<SUN 203>.A<N1 9> does not have a type.
FATAL: Atom .R<SUN 203>.A<C2 10> does not have a type.
FATAL: Atom .R<SUN 203>.A<C1 11> does not have a type.
FATAL: Atom .R<SUN 203>.A<O2 12> does not have a type.
FATAL: Atom .R<SUN 203>.A<C3 13> does not have a type.
FATAL: Atom .R<SUN 203>.A<C4 14> does not have a type.
I was thinking about using the RED program but I am not quite sure how
to prepare the right pdb file ... Could someone help me with this?
/Urszula
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Received on Fri Dec 09 2011 - 04:30:02 PST
