Hi,
The last two atoms (with no MM_NO) are the link-atoms.
I would suggest changing the position of the second link-atom; right now,
it is placed between the amide N and CA of residue 62 (potentially quite a
polar bond).
--Marc
On 16 May 2014 11:05, James Starlight <jmsstarlight.gmail.com> wrote:
> 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
> >>>> > 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 - 04:00:03 PDT
