Dear Amber experts
After reducing all hydrogen from the pdb file, I ran leap but it is ending
with the error
FATAL: Atom .R<LY 703>.A<N 1> does not have a type.
FATAL: Atom .R<LY 703>.A<CA 2> does not have a type.
FATAL: Atom .R<LY 703>.A<CB 3> does not have a type.
FATAL: Atom .R<LY 703>.A<CG 4> does not have a type.
FATAL: Atom .R<LY 703>.A<CD 5> does not have a type.
FATAL: Atom .R<LY 703>.A<CE 6> does not have a type.
FATAL: Atom .R<LY 703>.A<NZ 7> does not have a type.
FATAL: Atom .R<LY 703>.A<C 8> does not have a type.
FATAL: Atom .R<LY 703>.A<O 9> does not have a type.
FATAL: Atom .R<AS 704>.A<N 1> does not have a type
Failed to generate parameters
Parameter file was not saved.
I have also made following changes to the file
1. Edited PDB file
2. Reduced the PDB to delete all hydrogens
2. Added TER card after reducing
The steps in tleap are
source leaprc.ff99SB
var=loadpdb .pdb
saveAmberParm var .top .crd
quit
Please help me.
Wishes
*Krati Sharma
Research scholar
**
*
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Received on Mon Aug 05 2013 - 09:00:03 PDT
