[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
mark.j.abraham at gmail.com
Fri Jun 16 09:24:07 CEST 2017
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
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
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