Thanks Dan,
using -at amber have reduced output only to two errors
Checking for angle parameters.
Could not find angle parameter: C - N - CM
Could not find angle parameter: HA - C - N
There are missing parameters.
I dont know exactly to what CM and HA atoms can be changed in accordance
to standard a.a names in case of my chromophore so I'll try to add its
manually
James
2014-05-14 20:42 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Wed, May 14, 2014 at 9:55 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > using pdb w/o duplicate coordinates I've obtained flowing warnings during
> > parametrization of the GFP
> >
> > Checking parameters for unit 'dsRED'.
> > Checking for bond parameters.
> > Could not find bond parameter for: C - nh
>
> This happens because you are using Amber protein FF atom types (all
> upper-case) in your protein, GAFF atom types (all lower-case) in your
> ligand, and they are covalently bound; neither FF has these 'mixed'
> terms. You could try and force the ligand atom types to be Amber atom
> types (-at amber) and see if that helps; however, probably your best
> bet will be to try and assign these parameters by analogy, i.e. you
> will have to look in gaff.dat and for example find the 'c - n' bond
> parameter and create a frcmod file using that parameter as 'c - N',
> etc.
>
> Note that this kind of parameterization is advanced, and you should
> make sure that when assigning parameters this way that you understand
> and can explicitly justify how/why.
>
> Good luck,
>
> -Dan
>
> > Could not find bond parameter for: c - N
> > Checking for angle parameters.
> > Could not find angle parameter: O - C - nh
> > Could not find angle parameter: C - nh - c2
> > Could not find angle parameter: C - nh - hn
> > Could not find angle parameter: C - nh - hn
> > Could not find angle parameter: CT - C - nh
> > Could not find angle parameter: h4 - c - N
> > Could not find angle parameter: o - c - N
> > Could not find angle parameter: c - N - H
> > Could not find angle parameter: c - N - CT
> > Could not find angle parameter: c3 - c - N
> > There are missing parameters.
> > check: Warnings: 31
> >
> > from this you can find that amber doesn't recognize bonds and angles
> > between amino acid atoms and chromophore termi (nh and c atoms which has
> > been obtained such naming schemes automatically). Taking into account
> that
> > connection of my chromophore to the rest of the protein should be as the
> > regular peptide bond how I could define it explicitly ? (for example does
> > it possible to rename nh to N, c to C or some other solutions)?
> >
> > James
> >
> >
> > 2014-05-14 19:20 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> >
> >> The following error has been occurred during parametrization of the
> >> entirely protein using
> >> source leaprc.ff99SB
> >> source leaprc.gaff
> >> loadoff crq.lib # lib for chromophore
> >> dsRED = loadpdb 1zgo.pdb # pdb of the GFP w/o hydrogens
> >> bond dsRED.65.C dsRED.66.N # link N of chromophore to the C of previous
> >> residue
> >> bond dsRED.69.N dsRED.66.C # link C of chromophore to the N of next
> residue
> >>
> >>
> >>
> >> ERROR: Comparing atoms
> >> .R<CRQ 66>.A<CA3 4>,
> >> .R<CRQ 66>.A<O 6>,
> >> .R<CRQ 66>.A<HC4 27>, and
> >> .R<CRQ 66>.A<HC5 28>
> >> to atoms
> >> .R<CRQ 66>.A<CA3 4>,
> >> .R<SER 1>.A<N 1>,
> >> .R<CRQ 66>.A<O 6>, and
> >> .R<CRQ 66>.A<HC4 27>
> >> This error may be due to faulty Connection atoms.
> >> !FATAL ERROR----------------------------------------
> >> !FATAL: In file [chirality.c], line 142
> >> !FATAL: Message: Atom named N from SER did not match !
> >> !
> >> !ABORTING.
> >>
> >> This might be due to the presence of the alternative coppies of some
> atoms
> >> in the initial pdb which has been warned by amber
> >>
> >> Loading PDB file: ./1zgo.pdb
> >> -- residue 21: duplicate [ CB] atoms (total 2)
> >> -- residue 21: duplicate [ CG2] atoms (total 2)
> >> -- residue 21: duplicate [ OG1] atoms (total 2)
> >> -- residue 65: duplicate [ C] atoms (total 2)
> >> -- residue 65: duplicate [ CA] atoms (total 2)
> >> -- residue 65: duplicate [ O] atoms (total 2)
> >> -- residue 66: duplicate [ C1] atoms (total 2)
> >> -- residue 66: duplicate [ CA1] atoms (total 2)
> >> -- residue 66: duplicate [ CB1] atoms (total 2)
> >> -- residue 66: duplicate [ N] atoms (total 2)
> >> -- residue 66: duplicate [ N2] atoms (total 2)
> >> -- residue 66: duplicate [ N3] atoms (total 2)
> >> -- residue 67: duplicate [ CB] atoms (total 2)
> >> -- residue 67: duplicate [ OG] atoms (total 2)
> >>
> >> Warning: Atom names in each residue should be unique.
> >> (Same-name atoms are handled by using the first
> >> occurrence and by ignoring the rest.
> >> Frequently duplicate atom names stem from alternate
> >> conformations in the PDB file.)
> >>
> >>
> >> for instance next to the chromophore Ser:
> >>
> >> ATOM 521 N SER A 69 18.097 -19.121 43.129 1.00
> >> 16.45 N
> >> ANISOU 521 N SER A 69 2024 2279 1948 255 443
> >> 327 N
> >> ATOM 522 CA SER A 69 18.107 -19.900 44.359 1.00
> >> 15.64 C
> >> ANISOU 522 CA SER A 69 1746 2573 1624 320 841
> >> 158 C
> >> ATOM 523 C SER A 69 18.099 -18.961 45.552 1.00
> >> 17.01 C
> >> ANISOU 523 C SER A 69 2148 2306 2010 410 627
> >> 5 C
> >> ATOM 524 O SER A 69 18.979 -19.020 46.424 1.00
> >> 18.95 O
> >> ANISOU 524 O SER A 69 2315 2556 2328 469 366
> >> -403 O
> >> ATOM 525 CB ASER A 69 19.342 -20.803 44.326 0.61
> >> 18.43 C
> >> ANISOU 525 CB ASER A 69 2420 2848 1736 925 435
> >> 55 C
> >> ATOM 526 CB BSER A 69 19.323 -20.829 44.377 0.39
> >> 15.10 C
> >> ANISOU 526 CB BSER A 69 1914 2420 1402 383 1013
> >> 460 C
> >> ATOM 527 OG ASER A 69 19.430 -21.790 45.329 0.61
> >> 19.53 O
> >> ANISOU 527 OG ASER A 69 2960 2192 2268 230 -145
> >> -11 O
> >> ATOM 528 OG BSER A 69 20.482 -20.100 44.010 0.39
> >> 14.94 O
> >> ANISOU 528 OG BSER A 69 2035 1880 1762 687 1569
> >> 455 O
> >>
> >>
> >> how to ignore all alternative coordinates and fix it?
> >>
> >> TFH,
> >> James
> >>
> >>
> >> 2014-05-14 16:12 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> >>
> >> On Wed, 2014-05-14 at 13:00 +0100, Marc van der Kamp wrote:
> >>> > Just a minor addition to Jasons answer:
> >>> > There is one type of MM parameter that is not irrelevant for the QM
> >>> atoms:
> >>> > the non-bonded van der Waals parameters. These are used for the van
> der
> >>> > Waals interactions between MM and QM atoms.
> >>> > For most purposes, the atomtyping done by antechamber should be
> >>> sufficient.
> >>>
> >>> An important clarification. Thanks.
> >>>
> >>> Jason
> >>>
> >>> --
> >>> Jason M. Swails
> >>> BioMaPS,
> >>> Rutgers University
> >>> Postdoctoral Researcher
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu May 15 2014 - 03:00:02 PDT
