AMBER: Ligand problem

From: <>
Date: Mon, 19 Dec 2005 17:40:22 PDT
('binary' encoding is not supported, stored as-is)
Hello, Amber:

I try to creat the .parmtop and inpcrd files for my protein model. The
model is in .pdb file, and contains a cholesterol that was docked into
the protein. Here is how I did:

guanine.4% antechamber -i chol2.pdb -fi pdb -o chol2.prep -fo prepi

guanine.5% parmchk -i chol2.prep -f prepi -o chol2.parm

Then I load all the files:

guanine.6% $AMBERHOME/exe/tleap
> source leaprc.ff94
> source leaprc.gaff
> mod = loadamberparams frcmod-2
> loadamberprep chol2.prep
> loadamberparams chol2.parm

Here is the problem:

> test = loadpdb n62ch1.pdb
Loading PDB file: ./n62ch1.pdb
-- residue 1: duplicate [C] atoms (total 27)
-- residue 1: duplicate [H] atoms (total 46)

     (same-name atoms are reduced to a single atom)

Bond: maximum coordination exceeded on .R<UNK 1>.A<C 71>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<UNK 1>.A<C 71> .R<UNK 1>.A<O 5>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 443
!FATAL: Message: bondAtomProblem found

Can any one give me some advices on how to fix the problem? I have
included the files as attachments.

Your help will be very appreciated!


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Received on Tue Dec 20 2005 - 00:53:01 PST
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