AMBER Archive (2006)

Subject: Re: AMBER: NAD ??

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Nov 08 2006 - 09:55:38 CST

Hi,

To be more specific to what Prof. Case says, following is an example to what your pdb file looks like. If you had NDP residue alone in your pdb file, then xleap would not have a problem with NDP's atom coordinates. However, you have a TER card placed in between protein and NDP. In that case, the pdb format of NDP should conform with the pdb format of the protein.

ATOM 2298 CG LEU 319 27.999 128.267 54.811 1.00 0.00 C
ATOM 2299 CD1 LEU 319 27.226 128.530 53.525 1.00 0.00 C
ATOM 2300 CD2 LEU 319 28.149 129.529 55.656 1.00 0.00 C
TER
ATOM 2310 P1 NDP 320 29.167 148.439 45.205 1.00 0.00 P1+
ATOM 2311 O1 NDP 320 29.899 148.499 46.507 1.00 0.00 O1-
ATOM 2312 O2 NDP 320 29.176 149.723 44.453 1.00 0.00 O1-
ATOM 2313 O1 NDP 320 27.731 147.810 45.323 1.00 0.00 O

That is, your pdb file should look something like the following format:

ATOM 2298 CG LEU 319 27.999 128.267 54.811 1.00 0.00 C
 ATOM 2299 CD1 LEU 319 27.226 128.530 53.525 1.00 0.00 C
 ATOM 2300 CD2 LEU 319 28.149 129.529 55.656 1.00 0.00 C
 TER
 ATOM 2310 P1 NDP 320 29.167 148.439 45.205 1.00 0.00 P1+
 ATOM 2311 O1 NDP 320 29.899 148.499 46.507 1.00 0.00 O1-
 ATOM 2312 O2 NDP 320 29.176 149.723 44.453 1.00 0.00 O1-
 ATOM 2313 O1 NDP 320 27.731 147.810 45.323 1.00 0.00 O

See! everything is nicely lined-up here.

jenk.

Urszula Uciechowska <urszula.uciechowska_at_pharmazie.uni-halle.de> wrote:

Dear Amber Users,

I am trying to prepare a pdb with NAD to the xleap, but all the time I am getting such a
comments in xleap window and I have no idea how can I correct it? I tried many things but
always
I am getting the same..

This is what i got on the xleap window after loading pdb file

  ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Unknown residue: DP number: 314 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Creating new UNIT for residue: DP sequence: 320
Created a new atom named: 1 within residue: .R
Created a new atom named: 2 within residue: .R
Created a new atom named: 5 within residue: .R
Created a new atom named: 4 within residue: .R
Created a new atom named: 3 within residue: .R
Created a new atom named: 9 within residue: .R
Created a new atom named: 8 within residue: .R
Created a new atom named: 7 within residue: .R

I attached my pdb file.

Thanks for your patiente and looking forward for suggestions.

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg

 
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