AMBER Archive (2005)

Subject: Re: AMBER: antechamber problem

From: bybaker_at_itsa.ucsf.edu
Date: Wed Dec 21 2005 - 23:39:24 CST

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Dear Ilyas:

Thank you very much for your advices.

The 'n62ch1.pdb' file was generated from Dock program. I added one of the
ligand conformation into the protein pdb file using text, and then
re-save it using SwissPDB Viewer. That is why there are many other
information there.

I cleard up the pdb file: delete the REMARK, CONECT, SPDBVl and COMPND,
and leave the ligand and protein information there, then try it with
"tleap'. This time, the progeam complains: 

----
> 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_at_scripps.edu on behalf of Ilyas Yildirim
Sent:   Tue 12/20/2005 4:39 PM
To:     amber_at_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_at_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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