[AMBER] ligand parameterization

From: gurunath katagi <gurukatagi.gmail.com>
Date: Wed, 24 Mar 2010 11:35:24 +0530

Dear all,
I have done docking of a protein with a ligand molecule. Aftre docking , the
ligand pdbqt files generated , were coverted to pdb files and a protein
ligand complex was generated.
Now that , i want to parmeterize this lignad molecule using antechmber and
run the simulation on this complex.

I am getting the folowing error when i run the antechmber program :
Checking Unit.
WARNING: There is a bond of 8.963830 angstroms between:
------- .R<GLY 82>.A<C 6> and .R<ARG 83>.A<N 1>
WARNING: There is a bond of 5.926085 angstroms between:
------- .R<GLN 125>.A<C 16> and .R<ARG 126>.A<N 1>
FATAL: Atom .R<UNK 269>.A<O 1> does not have a type.
FATAL: Atom .R<UNK 269>.A<H6 2> does not have a type.
FATAL: Atom .R<UNK 269>.A<C3 3> does not have a type.
FATAL: Atom .R<UNK 269>.A<O1 4> does not have a type.
FATAL: Atom .R<UNK 269>.A<C2 5> does not have a type.
FATAL: Atom .R<UNK 269>.A<N 6> does not have a type.
FATAL: Atom .R<UNK 269>.A<H 7> does not have a type.
FATAL: Atom .R<UNK 269>.A<H1 8> does not have a type.
FATAL: Atom .R<UNK 269>.A<H2 9> does not have a type.
FATAL: Atom .R<UNK 269>.A<H5 10> does not have a type.
FATAL: Atom .R<UNK 269>.A<C1 11> does not have a type.
FATAL: Atom .R<UNK 269>.A<H3 12> does not have a type.
FATAL: Atom .R<UNK 269>.A<H4 13> does not have a type.
FATAL: Atom .R<UNK 269>.A<S 14> does not have a type.
FATAL: Atom .R<UNK 269>.A<C 15> does not have a type.
FATAL: Atom .R<UNK 269>.A<C10 16> does not have a type.
FATAL: Atom .R<UNK 269>.A<C11 17> does not have a type.
FATAL: Atom .R<UNK 269>.A<C12 18> does not have a type.
FATAL: Atom .R<UNK 269>.A<C13 19> does not have a type.
FATAL: Atom .R<UNK 269>.A<C14 20> does not have a type.
FATAL: Atom .R<UNK 269>.A<C15 21> does not have a type.
FATAL: Atom .R<UNK 269>.A<H15 22> does not have a type.
FATAL: Atom .R<UNK 269>.A<H14 23> does not have a type.
FATAL: Atom .R<UNK 269>.A<H13 24> does not have a type.
FATAL: Atom .R<UNK 269>.A<H12 25> does not have a type.
FATAL: Atom .R<UNK 269>.A<H11 26> does not have a type.
FATAL: Atom .R<UNK 269>.A<C16 27> does not have a type.
FATAL: Atom .R<UNK 269>.A<C17 28> does not have a type.
FATAL: Atom .R<UNK 269>.A<C18 29> does not have a type.
FATAL: Atom .R<UNK 269>.A<C19 30> does not have a type.
FATAL: Atom .R<UNK 269>.A<C20 31> does not have a type.
FATAL: Atom .R<UNK 269>.A<C21 32> does not have a type.
FATAL: Atom .R<UNK 269>.A<H20 33> does not have a type.
FATAL: Atom .R<UNK 269>.A<H19 34> does not have a type.
FATAL: Atom .R<UNK 269>.A<H18 35> does not have a type.
FATAL: Atom .R<UNK 269>.A<H17 36> does not have a type.
FATAL: Atom .R<UNK 269>.A<H16 37> does not have a type.
FATAL: Atom .R<UNK 269>.A<C4 38> does not have a type.
FATAL: Atom .R<UNK 269>.A<C5 39> does not have a type.
FATAL: Atom .R<UNK 269>.A<H7 40> does not have a type.
FATAL: Atom .R<UNK 269>.A<C6 41> does not have a type.
FATAL: Atom .R<UNK 269>.A<H8 42> does not have a type.
FATAL: Atom .R<UNK 269>.A<C7 43> does not have a type.
FATAL: Atom .R<UNK 269>.A<Br 44> does not have a type.
FATAL: Atom .R<UNK 269>.A<C8 45> does not have a type.
FATAL: Atom .R<UNK 269>.A<H9 46> does not have a type.
FATAL: Atom .R<UNK 269>.A<C9 47> does not have a type.
FATAL: Atom .R<UNK 269>.A<H10 48> does not have a type.
Failed to generate parameters
Parameter file was not saved.
> quit
The following proceudre was followed :

antechamber -i lig2.pdb -fi pdb -o lig2.prepin -fo prepi -nc -1 -m 1 -c bcc
-s 2
/amber9/exe/parmchk -i lig2.prepin -f prepi -o lig.frcmod

$AMBERHOME/xleap -s /amber9/dat/leap/cmd/leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 lig2.prepin
check LIG
loadamberparams lig.frcmod
check LIG
savepdb LIG lig12.pdb
complex = loadpdb c2.pdb
check complex
savepdb complex complex1.pdb
addions complex Na+ 0
solvatebox complex TIP3PBOX 10.0
savepdb complex complex_box.pdb
saveamberparm complex cmplx.prmtop cmplx.inpcrd
quit
I have attached the required files to run this program.
NCI44.pdb_ligand_01.pdbqt -- output from docking proogram. this is ligand
pdbqt files
lig2.pdb -- lignad pdb file used to tun the antechenber program
c2.pdb -- protein-ligand complex

 Kindly look into it and suggest me as to how I should proceed .

Thank you
Gurunath M Katagi
Graduate Research Student
Bio molecular computation Laboratory
Supercomputer Education & Research Center
Indian Institute Of Science, Bangalore- 560012
Karnataka State, India
Phone:080-22932737-319,080-22933061
email: gurunath.rishi.serc.iisc.ernet.in


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Received on Tue Mar 23 2010 - 23:30:03 PDT
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