AMBER Archive (2006)

Subject: Re: AMBER: NAD ??

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Fri Nov 10 2006 - 03:36:15 CST

hi,

I corrected my pdb file, but now I am getting the errors like

WARNING: There is a bond of 3.897415 angstroms between:
------- .R<NDP 320>.A<P1 1> and .R<NDP 320>.A<O3 4>
WARNING: The unperturbed charge of the unit: 1.999898 is not zero.
FATAL: Atom .R<NDP 320>.A<P 73> does not have a type.
FATAL: Atom .R<NDP 320>.A<N9 74> does not have a type.
FATAL: Atom .R<NDP 320>.A<NP 75> does not have a type.
FATAL: Atom .R<NDP 320>.A<NO1 76> does not have a type.
FATAL: Atom .R<NDP 320>.A<NO2 77> does not have a type.
FATAL: Atom .R<NDP 320>.A<NO5 78> does not have a type.
FATAL: Atom .R<NDP 320>.A<NC5 79> does not have a type.

and ...

Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C18-N7-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C21-N6-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes

I attached my pdb.

Thanks for your patiente and looking forward for suggestions.

Best Regards,
Urszula Uciechowska

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

----- Original Message -----
From: Cenk Andac <cenk_andac_at_yahoo.com>
Date: Wednesday, November 8, 2006 5:12 pm
Subject: Re: AMBER: NAD ??
To: amber_at_scripps.edu

> 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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