[gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Mark Abraham]

Hi,

You need to understand how AMBER uses the contents of the prm file, and how
to produce suitable .rtp and atom type entries for use with GROMACS. This
will mean some spending some quality time with the documentation. That's
one reason that such simulations are not a good idea for someone learning
how to do molecular simulations.

Mark

On Tue, Jun 27, 2017 at 6:06 AM Rana Rehan Khalid <rrkhalid at umich.edu>
wrote:

> Hi
> I have ff of heme fe---o2  some one use it before these are amber heme ff
> he use amber 99sb and this heme ff in his md  simulation  but he done his
> work in amber. Can you guide me that how I can use this heme ff of amber in
> combination with amber99sb  at number 6 position in gromacs
>
> On Jun 14, 2017 4:55 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>
> On 6/14/17 12:25 AM, Rana Rehan Khalid wrote:
>
> > Hi
> > I have read the chapter 5 of manual but i am confuse how can i add
> residue
> > into heme atom of .rtp ff
> > this is the coordinate due to which error come
> >
> > HETATM 1529  O01 HEM   187       3.996  19.101  70.594  0.00
> > 0.00           O
> >
> > kindly guide me how i can make changes in the rtp file and .atp so that
> > this error remove
> > here is the heme rtp part of my selected ff where i can add O01 and also
> > tell me these 4 column and these values and tell me which value i add for
> > O01 like (FE FE 0.40000     0 )
> >
>
> You should refer back to the manual if the contents of these files are not
> clear.  You're seeking to introduce new parameters for an oxygen-bound form
> of heme; this may require very complex parametrization work.  Modifying an
> .rtp file is trivial; it's just text.  Putting realistic parameters into it
> is a whole other matter.  Check the literature for any existing efforts to
> avoid duplicated work.
>
> -Justin
>
>
> [ HEME ]
> >   [ atoms ]
> >     FE    FE     0.40000     0
> >     NA    NR    -0.10000     0
> >     NB    NR    -0.10000     0
> >     NC    NR    -0.10000     0
> >     ND    NR    -0.10000     0
> >    CHA     C    -0.10000     1
> >    HHA    HC     0.10000     1
> >    C1A     C     0.00000     2
> >    C2A     C     0.00000     2
> >    C3A     C     0.00000     2
> >    C4A     C     0.00000     2
> >    CMA   CH3     0.00000     3
> >    CAA   CH2     0.00000     4
> >    CBA   CH2     0.00000     4
> >    CGA     C     0.27000     5
> >    O1A    OM    -0.63500     5
> >    O2A    OM    -0.63500     5
> >    CHB     C    -0.10000     6
> >    HHB    HC     0.10000     6
> >    C1B     C     0.00000     7
> >    C2B     C     0.00000     7
> >    C3B     C     0.00000     7
> >    C4B     C     0.00000     7
> >    CMB   CH3     0.00000     8
> >    CAB   CR1     0.00000     9
> >    CBB   CH2     0.00000     9
> >    CHC     C    -0.10000    10
> >    HHC    HC     0.10000    10
> >    C1C     C     0.00000    11
> >    C2C     C     0.00000    11
> >    C3C     C     0.00000    11
> >    C4C     C     0.00000    11
> >    CMC   CH3     0.00000    12
> >    CAC   CR1     0.00000    13
> >    CBC   CH2     0.00000    13
> >    CHD     C    -0.10000    14
> >    HHD    HC     0.10000    14
> >    C1D     C     0.00000    15
> >    C2D     C     0.00000    15
> >    C3D     C     0.00000    15
> >    C4D     C     0.00000    15
> >    CMD   CH3     0.00000    16
> >    CAD   CH2     0.00000    17
> >    CBD   CH2     0.00000    17
> >    CGD     C     0.27000    18
> >    O1D    OM    -0.63500    18
> >    O2D    OM    -0.63500    18
> >
> > thanks
> >
> >
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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