Hi Marc,
Many thanks for suggestions! The inclusion of the side chain's atoms to the
QM mask have been solved my problem.
Could you also tell me
1) What the information from the initial ff parameters of my QM group taken
from the prmtop would be most meaningful for the qm/mm simulation.
Previously you've mentioned that this information will be ignored during
qm/mm run but it seem that initial molecular 3D geometry and charge
distribution have some matter, haven't it?
2) What are the most reasonable methods and tools for the analysis of QM/MM
trajectories ? On what dynamical properties of simulated system should I
paid most of attention? E.g the most trivial is the analysis of the 3D
geometry during simulation. How can I make such analysis obtaining both
visualization and numerical values (E.g torsion angles in
functional-relevant groups)? Does it possible to calculate charge density
for those groups as well?
James
2014-05-16 15:18 GMT+04:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> Hi,
> If you decide to add in CA, you also need to add in the atoms attached to
> it (HA and the whole side-chain, or have another link-atom in the
> side-chain). Is there no good non-polar bond in your chromophore 'backbone'
> perhaps?
> --Marc
>
>
> On 16 May 2014 11:45, James Starlight <jmsstarlight.gmail.com> wrote:
>
> > adding CA atom to the second selection have resulted in the
> >
> > QMMM: System specified with odd number of electrons ( 145)
> > QMMM: but odd spin ( 1). You most likely have the charge of
> > QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> > calculation.
> >
> >
> > Does it mean that I should provide positive total charge to the qm region
> > in that case? How it could be accurately calculated?
> >
> >
> > 2014-05-16 14:39 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> >
> > > 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
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun May 18 2014 - 04:00:02 PDT
