AMBER Archive (2005)

Subject: AMBER: Re: Ligand problem

From: bybaker_at_itsa.ucsf.edu
Date: Tue Dec 20 2005 - 12:50:03 CST

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Dear Lawel:

Thank you for your suggestion.

I compare the .prep file with the .pdb file. The ligand name in the pdb
file (the third row) is the same as in the .prep file. Both are 'UNK'. In
the .pdb file, the ligand atoms are named 'UNK' and '1' (the 4th row). I
then try to change the name to "UNK 1" in my .prep file, but this causes
the same problem as before.

I notice that there are three dumm atoms in the .prep file. This makes
the total atom numbers to 77 in the .prep file. But in the .pdb file,
there are 74 total atoms for the ligand. Does this is the cause of the
problem? As the 'leap' complaines: 

----
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
!
!ABORTING.
----

I use the 'antechamber' to generate the .prep file, and Amber7. 

Thank you for you advices

Bo 

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.
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)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (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
!
!ABORTING.

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!

Bo

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