Hi Jenk,
Thanks a lot for your emails and help, its still not working with me and i have no idea what i am doing wrong,
i am quite sure that most of my atoms are containing the prefix "N" i checked it in the orginal pdb file to be
sure. I am still getting fatal errors that my atoms dont have a type ....
I think that my atom names from pdb dont match exactly to the NDP.lib and i have no idea how to change it. How
can I create in easy way a lib file?
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.yahoo.com>
Date: Saturday, November 11, 2006 0:30 am
Subject: Re: AMBER: NAD ??
To: amber.scripps.edu
> Hi Urszula,
>
> I have lined-up columns for the NDP part of your pdb
> file as follows.
>
> ATOM 2310 P1 NDP 3003 29.167 148.439 45.205
> 1.00 0.00 P1+
> ATOM 2311 O1 NDP 3003 29.899 148.499 46.507
> 1.00 0.00 O1-
> ATOM 2312 O2 NDP 3003 29.176 149.723 44.453
> 1.00 0.00 O1-
> ATOM 2313 O5 NDP 3003 27.731 147.810 45.323
> 1.00 0.00 O
> ATOM 2314 C5 NDP 3003 27.479 146.626 46.009
> 1.00 0.00 C
> ATOM 2315 C4 NDP 3003 26.050 146.686 46.427
> 1.00 0.00 C
> ATOM 2316 O4 NDP 3003 25.848 145.446 47.041
> 1.00 0.00 O
> ATOM 2317 C3 NDP 3003 25.731 147.810 47.439
> 1.00 0.00 C
> ATOM 2318 O3 NDP 3003 24.577 148.523 47.043
> 1.00 0.00 O
> ATOM 2319 C2 NDP 3003 25.522 147.020 48.728
> 1.00 0.00 C
> ATOM 2320 O2 NDP 3003 24.602 147.627 49.631
> 1.00 0.00 O
> ATOM 2321 C1 NDP 3003 25.045 145.667 48.158
> 1.00 0.00 C
> ATOM 2322 N9 NDP 3003 25.085 144.576 49.126
> 1.00 0.00 N
> ATOM 2323 C8 NDP 3003 26.134 144.261 49.956
> 1.00 0.00 C
> ATOM 2324 N7 NDP 3003 25.723 143.220 50.706
> 1.00 0.00 N
> ATOM 2325 C5 NDP 3003 24.453 142.874 50.402
> 1.00 0.00 C
> ATOM 2326 C6 NDP 3003 23.579 141.916 50.880
> 1.00 0.00 C
> ATOM 2327 N6 NDP 3003 23.924 141.051 51.809
> 1.00 0.00 N
> ATOM 2328 N1 NDP 3003 22.340 141.805 50.342
> 1.00 0.00 N
> ATOM 2329 C2 NDP 3003 21.954 142.665 49.325
> 1.00 0.00 C
> ATOM 2330 N3 NDP 3003 22.812 143.622 48.856
> 1.00 0.00 N
> ATOM 2331 C4 NDP 3003 24.051 143.723 49.391
> 1.00 0.00 C
> ATOM 2332 O3 NDP 3003 30.110 147.509 44.275
> 1.00 0.00 O
> ATOM 2333 NP NDP 3003 29.971 147.257 42.671
> 1.00 0.00 P1+
> ATOM 2334 NO1 NDP 3003 30.972 148.085 41.976
> 1.00 0.00 O1-
> ATOM 2335 NO2 NDP 3003 28.511 147.270 42.357
> 1.00 0.00 O1-
> ATOM 2336 NO5 NDP 3003 30.551 145.710 42.573
> 1.00 0.00 O
> ATOM 2337 NC5 NDP 3003 29.787 144.618 43.016
> 1.00 0.00 C
> ATOM 2338 NC4 NDP 3003 30.577 143.292 42.824
> 1.00 0.00 C
> ATOM 2339 NO4 NDP 3003 30.760 142.967 41.439
> 1.00 0.00 O
> ATOM 2340 NC3 NDP 3003 31.975 143.358 43.421
> 1.00 0.00 C
> ATOM 2341 NO3 NDP 3003 32.190 142.166 44.137
> 1.00 0.00 O
> ATOM 2342 NC2 NDP 3003 32.893 143.490 42.239
> 1.00 0.00 C
> ATOM 2343 NO2 NDP 3003 34.247 143.094 42.393
> 1.00 0.00 O
> ATOM 2344 NC1 NDP 3003 32.118 142.619 41.225
> 1.00 0.00 C
> ATOM 2345 NN1 NDP 3003 32.457 142.862 39.837
> 1.00 0.00 N1+
> ATOM 2346 NC2 NDP 3003 32.422 141.773 38.970
> 1.00 0.00 C
> ATOM 2347 NC3 NDP 3003 32.657 141.946 37.614
> 1.00 0.00 C
> ATOM 2348 NC7 NDP 3003 32.649 140.738 36.684
> 1.00 0.00 C
> ATOM 2349 NO7 NDP 3003 33.262 140.889 35.448
> 1.00 0.00 O
> ATOM 2350 NN7 NDP 3003 32.081 139.596 37.054
> 1.00 0.00 N
> ATOM 2351 NC4 NDP 3003 32.945 143.231 37.107
> 1.00 0.00 C
> ATOM 2352 NC5 NDP 3003 32.948 144.324 37.992
> 1.00 0.00 C
> ATOM 2353 NC6 NDP 3003 32.688 144.120 39.351
> 1.00 0.00 C
> TER 2354 NDP 3003
> END
>
>
> It did however catch my attention that there are some
> duplicate atom names in your pdb file. You may want to
> check out NDP.lib and see if atom names therein match
> those in your pdb file...Also, are you really sure
> that
> most atom names takes the prefix "N" ???
>
> hope that helps..
>
>
> jenk.
>
>
>
>
>
> --- Urszula Uciechowska
> <urszula.uciechowska.pharmazie.uni-halle.de> wrote:
>
> >
> > 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.yahoo.com>
> > Date: Wednesday, November 8, 2006 5:12 pm
> > Subject: Re: AMBER: NAD ??
> > To: amber.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.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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> > >
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> >
> === message truncated ===
>
>
>
>
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Received on Wed Nov 15 2006 - 06:07:12 PST
