There are several problems here.
1) Your protein needs to have all hydrogens present (Amber is an all-atom
force field.) Your protein structure doesn't have ANY hydrogens. They need
to be there.
(you probably used Autodock, or some program that only uses polar
hydrogens...)
2) The structure of your ligand is not docked to the protein in your complex
so it doesn't appear that the docking program did any docking, or you were
not careful about how you saved the docked coordinates.
3) The structure of your ligand in your ligand file is a VERY high energy
structure, it looks as if you built it by hand. That structure needs to be
minimized to a more realistic conformation, the benzene rings will never be
perpendicular like you have them.
4) The protonated carboxyl you have will be the predominant species only at
pH's well below 2. If you plan to be working near physiologic pH, then you
need to have the correct ionic species that exists near physiologic pH.
I suggest you do the tutorials and consider VERY carefully the chemistry and
details of the structures you are working with before you even begin doing
any MD. Otherwise it's all a crap shoot.
For example,
Have you protonated your protein and determined which protonation state or
annular tautomeric state you need to assign for each of the histidines in
your protein using the reduce program, or the H++ server? (Remember, there
are 3 different structures possible for histidine near physiologic pH)?
Have you used Molprobity or WhatCheck to determine if there are any Asn,
Gln, or His that need to be flipped because they were incorrectly assigned
in the original published structure?
I hope this inspires you to dig further by reading the archives of this list
to learn more before you spend a lot of cpu time on meaningless structures.
With best regards,
Dean
-- "It is the mark of an educated mind to be able to
entertain a thought without accepting it." -- Aristotle
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: gurunath katagi <gurukatagi.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Wed, 24 Mar 2010 01:05:24 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] ligand parameterization
>
> 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 Wed Mar 24 2010 - 11:00:03 PDT
