Thanks Marc!
James
2014-05-16 14:33 GMT+04:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> 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
> > >>>>
> > >>>
> > >>>
> > >>
> > >
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 16 2014 - 04:00:04 PDT
