It seems that I've found possible source of the error: HA was the extra
atom wrongly bonded to the C during the parametrization of the residue
(making terminal COH group instead of COOH).
Should I cap my non standard residue from N and C termi placing full
terminal NH2 groups COOH or alternatvely cut H or OH making -nc -1 flag ?
2014-05-15 13:33 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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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>>
>
>
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Received on Thu May 15 2014 - 04:30:03 PDT
