Re: AMBER: Ligand problem

From: <>
Date: Tue, 20 Dec 2005 02:02:54 +0100 (CET)

Dear Bo!
I think that you have to compare prep file with pdb. I guess you
do not have the same atom name. The third raw in pdb file have to
be the same in prep file (besides the dummy atoms). Besides
problem may be in the molecule name. Did you really named your
molecule UNK 1? See what is the name in pdb file (4th row), and
compare it with the name of molecule in prep file.
|awel Gruszczynski
Gdansk Uniwersity
Chemistry Departament
Hello, Amber:
I try to creat the .parmtop and inpcrd files for my protein model.
model is in .pdb file, and contains a cholesterol that was docked
the protein. Here is how I did:
guanine.4% antechamber -i chol2.pdb -fi pdb -o chol2.prep -fo
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 - 01:53:01 PST
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