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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--
-------------------------
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
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Received on Wed May 14 2014 - 10:00:03 PDT
