also a question regarding choosing of the atom mask for the QM part:
for my GFP system I've defined it as
qmmask=":CRQ|:60&.C,O|:62&.N,H" # selecting resname CRQ, CO from previous
residue and NH from the next residue
in the log I've found
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 956 C 1.4330 0.3888 5.3553
QMMM: 2 957 O 2.1733 -0.4414 5.8816
QMMM: 3 958 N 0.9279 0.0664 4.1462
QMMM: 4 959 C 0.5263 0.8671 2.9712
QMMM: 5 960 C -0.9975 0.5811 2.7132
QMMM: 6 961 C -1.7371 -0.2668 3.7905
QMMM: 7 962 C 1.5136 0.4979 1.8566
QMMM: 8 963 N 1.0344 0.5241 0.5266
QMMM: 9 964 N 2.9273 0.4873 1.9765
QMMM: 10 965 C 3.3404 0.4118 0.6441
QMMM: 11 966 O 4.4984 0.4328 0.2368
QMMM: 12 967 C 2.2282 0.5876 -0.1838
QMMM: 13 968 C 3.8085 0.2165 3.0816
QMMM: 14 969 C 2.3668 0.8069 -1.6133
QMMM: 15 970 C 1.4013 1.1850 -2.5796
QMMM: 16 971 C 0.0282 1.4052 -2.3355
QMMM: 17 972 C 1.8674 1.3408 -3.8761
QMMM: 18 973 C -0.8434 1.6555 -3.3373
QMMM: 19 974 C 0.9491 1.7019 -4.8596
QMMM: 20 975 C -0.4032 1.8833 -4.6305
QMMM: 21 976 O -1.1154 2.1264 -5.5666
QMMM: 22 977 O -3.9780 -1.2398 3.8832
QMMM: 23 978 C 3.6428 -1.2449 3.6140
QMMM: 24 979 O 4.4668 -1.7690 4.2991
QMMM: 25 980 C -3.2487 -0.3047 3.5743
QMMM: 26 981 N -3.9230 0.7299 3.0197
QMMM: 27 982 H -1.5021 1.5491 2.6870
QMMM: 28 983 H -1.1440 -0.0132 1.8089
QMMM: 29 984 H -1.4398 -0.0842 4.8252
QMMM: 30 985 H -1.4218 -1.2994 3.6266
QMMM: 31 986 H 3.6246 0.8901 3.9211
QMMM: 32 987 H 4.8392 0.3953 2.7682
QMMM: 33 988 H 3.3291 0.6685 -2.0996
QMMM: 34 989 H -0.4255 1.3772 -1.3481
QMMM: 35 990 H 2.8907 1.1751 -4.2032
QMMM: 36 991 H -1.9041 1.8307 -3.1768
QMMM: 37 992 H 1.3141 1.7642 -5.8816
QMMM: 38 993 H 0.7020 -0.9094 4.0238
QMMM: 39 994 H -3.5395 1.5972 2.6751
QMMM: 40 995 H -4.8392 0.4430 2.7092
QMMM: 41 996 N 2.9052 -2.1264 2.8504
QMMM: 42 997 H 2.2644 -1.6136 2.2634
QMMM: 43 *H 1.3730 1.4305 5.6706
QMMM: 44 *H 2.7072 -3.1827 3.0328
I've performed short simulation and visualized chromophore and didn't
noticed any artifacts. Does such selection seems correct? What are the last
tho *H atoms ?
James
2014-05-16 11:26 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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
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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 Fri May 16 2014 - 03:30:03 PDT
