[AMBER] problems with getting right parameters ...

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Fri, 9 Dec 2011 12:58:59 +0100

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
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