Try to explain my question:
If I parametrize my chromophore with capped N and C termi by NH2 and COOH
groups (in neutral form) and try to connect it to the rest of the protein
the H and OH (water) have not been removed automatically as in case of
typical peptide bond formation so in both of these regions N and C atoms
have wrong Sp3 geometry.
Should I parametrize my chromophore with already removed OH and H from both
termi (in form like it present in bonded form with the protein) defining -2
total charge
antechamber -i CRQ.pdb -fi pdb -o crq.mol2 -fo mol2 -c bcc -s 2 -at amb er
-nc -2
but assuming that in bonded form chromophore must be neutral?
James
2014-05-15 15:06 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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
>>> >>>
>>> >>
>>> >>
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > 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)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Fri May 16 2014 - 00:30:02 PDT
