[gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.
Rana Rehan Khalid
rrkhalid at umich.edu
Fri Jun 23 21:34:28 CEST 2017
Dear sir i have force field for O2 now some one work over it before its the
.prm file he use to run simulation amber99 force field and use there own
lab heme generated ff heme fe ----02 now how i can use these amber heme
force field in Gromacs thanks.
On Fri, Jun 16, 2017 at 3:23 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Generating a suitable model for such a system, plus its parameters, is a
> lot of work, generally unsuitable for a beginner, and IMO unlikely to work
> well. As I have suggested before, start by reading the literature for what
> others have done. Maybe your problem is solved, maybe it should not be
> attempted. :-)
>
> Mark
>
> On Fri, 16 Jun 2017 01:39 Rana Rehan Khalid <rrkhalid at umich.edu> wrote:
>
> > kindly tell me sir how i can i add residue
> >
> > On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid <rrkhalid at umich.edu>
> > wrote:
> >
> > > thanks justin
> > > actually i want to know that how these values of column (atom name,
> type,
> > > charge and charge group) we obtain for oxygen bonded with heme fe. is
> > there
> > > any program through which i find the parameter file for oxygen with
> heme
> > > and nitric oxide with heme iron. if i just add the atom name type and
> > > charge in the bonded type heme fe atoms is it work for me can you tell
> me
> > > about any tutorial in which adding residue shows with examples that
> will
> > be
> > > very understandable. thanks
> > >
> > > On Wed, Jun 14, 2017 at 4:54 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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