AMBER Archive (2006)

Subject: Re: AMBER: NAD ??

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Nov 13 2006 - 08:46:47 CST

Hi Urszula,

I think the best way to conform with lib or off files is to both run xleap on one console and run another viewer program (such as rasmol or vmd or chimera) on another console at the same time. This way you would have the best chance to compare your pdb and lib(off) file names. With the edit in xleap you can view, select and visuliaze your off/lib atom names, while you still have a chance to compare atom names in a pdb viewer on the other hand..

Another way to compare atom names in lib/off and pdb files is to load an off/lib file in xleap first (i.e.; "loadamberparams frcmod.nad" and then "mol=loadoff nad.lib" )and save a pdb file using the savepdb command in xleap (i.e.; "savepdb mol mol.pdb"). I would then compare these two pdb files (the one saved in xleap and your pdb file) in different windows of a viewer , i.e.; rasmol.

Also, make sure that you download the correct NAD lib and frcmod files off the AMBER contributors website at http://pharmacy.man.ac.uk/amber .

If you still think that thinks are not working properly, please feel free to send me in your NAD coordinates in your pdb file. I would be willing to help you prepare your pdb file in a way that xleap recognizes it with no problem.

regards,

jenk

Urszula Uciechowska <urszula.uciechowska_at_pharmazie.uni-halle.de> wrote:
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
Date: Saturday, November 11, 2006 0:30 am
Subject: Re: AMBER: NAD ??
To: amber_at_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
> 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.A
 and .R.A
> > WARNING: The unperturbed charge of the unit:
> > 1.999898 is not zero.
> > FATAL: Atom .R.A
 does not have a
> > type.
> > FATAL: Atom .R.A does not have a
> > type.
> > FATAL: Atom .R.A does not have a
> > type.
> > FATAL: Atom .R.A does not have a
> > type.
> > FATAL: Atom .R.A does not have a
> > type.
> > FATAL: Atom .R.A does not have a
> > type.
> > FATAL: Atom .R.A 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
> > 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
> >
> > > 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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> >
> === message truncated ===
>
>
>
>
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