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----
> molecule = loadpdb n62ch1c.pdb
Loading PDB file: ./n62ch1c.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)
Added missing heavy atom: .R<UNK 1>.A<C 65>
Added missing heavy atom: .R<UNK 1>.A<C 62>
Added missing heavy atom: .R<UNK 1>.A<C 66>
---
Added missing heavy atom: .R<UNK 1>.A<C 4>
Added missing heavy atom: .R<UNK 1>.A<C 1>
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 115
!FATAL: Message: No N in aaOrig list
!
!ABORTING.
----
As you mentioned,
>Each atom name should be unique. After doing this, create the new
.prep file which has the unique atom naming in it.
>
But, I notice that in the pdb file, atoms start from "C", then end with
"H". But in the .prep file, each "C" atom is followed by their "H". I use
'antechamber' (Amber7) to generate the .prep file from the choleterol pdb
file. I try the "babel" to generate a new "chol3a.pdb" from the oringinal
chol.pdb, but it is the same order as before: start with "C', then edn
with "H". I have attached the files. I am not sure this is the cause for
the problem in "tleap". It may be worth to fix this part first. Or I have
to mannually change all the atom type of ligand in the .pdb file? Is
there easy way to name the atoms in pdb file in order to match with that
in the .prep file?
Thank you for your advices.
All the best
Bo
-----Original Message-----
From: owner-amber.scripps.edu on behalf of Ilyas Yildirim
Sent: Tue 12/20/2005 4:39 PM
To: amber.scripps.edu
Cc:
Subject: Re: AMBER: Re: Ligand problem
Dear Bo,
I checked out the files you attached; chol2.parm, n62ch1.pdb, chol2.prep.
Where did u get the .pdb file? First thing I would suggest is to erase
all of the unnecessary information from the .pdb file. This includes the
REMARK, CONECT, SPDBVl and COMPND. Keep only ATOM, TER and END parts. But
still I wonder where u get this .pdb file, because the following line
looks very strange:
TER 3376 ALA 280
In any case, keep only the lines I suggested above. The reason why u are
getting the FATAL error is because of the CONECT lines. After
changing the .pdb file, create an xleap.in file like the following:
--------------- xleap.in -----------------------
source leaprc.ff99
loadamberparams chol2.parm
loadamberprep chol2.prep
molecule = loadpdb n62ch1_new.pdb
------------------------------------------------
When u use this file while running xleap ("xleap -f xleap.in") This will
load the .parm, .prep and the modified .pdb files in xleap. Still, u will
see a lot of errors. One of the error is
ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
U have to name each atom names uniquely, in the residues. Do the same
thing for 'chol2' structure. For instance, the 'chol' structure is defined
in your .pdb as follows:
------------------- n62ch1.pdb --------------------
.
.
.
ATOM 13 C UNK 1 26.249 36.985 22.805
ATOM 14 C UNK 1 25.320 37.058 24.198
ATOM 15 C UNK 1 24.122 39.487 20.962
ATOM 16 C UNK 1 24.777 38.790 19.778
ATOM 17 C UNK 1 25.849 37.616 20.433
ATOM 18 O UNK 1 21.836 38.854 29.441
ATOM 19 C UNK 1 22.749 37.025 25.359
ATOM 20 C UNK 1 23.963 36.666 21.878
ATOM 21 C UNK 1 25.666 36.293 19.700
ATOM 22 C UNK 1 26.346 35.179 20.485
ATOM 23 C UNK 1 26.286 36.390 18.313
ATOM 24 C UNK 1 25.606 37.503 17.528
ATOM 25 C UNK 1 26.226 37.601 16.140
ATOM 26 C UNK 1 25.546 38.713 15.355
ATOM 27 C UNK 1 26.166 38.810 13.967
ATOM 28 C UNK 1 25.726 40.037 16.087
ATOM 29 H UNK 1 22.727 36.908 27.948
ATOM 30 H UNK 1 24.036 37.412 29.084
ATOM 31 H UNK 1 23.524 39.816 28.622
.
.
.
-----------------------------------------------------
Each atom name should be unique. After doing this, create the new
.prep file which has the unique atom naming in it. I hope this will solve
your problem, or will let u get less error messages in xleap, which can
be solved easily.
Good luck,
On Tue, 20 Dec 2005 bybaker.itsa.ucsf.edu wrote:
> 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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>
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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