the mail you sent me today?? sir
On Mon, Jul 3, 2017 at 12:14 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> You need to model your O's. Probably good to read up on O2 modeling in
> Amber.
>
> Maybe you need to make O2 not be part of the heme? Is it bonded?
>
> If it's bonded, read my previous mail on the subject closely for
> instructions.
>
> Bill
>
>
> On 7/2/17 9:11 PM, Rana Rehan Khalid wrote:
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-FE-ND-*
> > +--- With Sp0 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > Created a new atom named: O01 within residue: .R<HEM 187>
> > Created a new atom named: O02 within residue: .R<HEM 187>
> > ERROR: Comparing atoms
> > .R<HEM 187>.A<ND 55>,
> > .R<HEM 187>.A<NC 39>,
> > .R<HEM 187>.A<NB 23>, and
> > .R<HEM 187>.A<NA 2>
> > to atoms
> > .R<HEM 187>.A<ND 55>,
> > .R<HEM 187>.A<NC 39>,
> > .R<HEM 187>.A<O1 74>, and
> > .R<HEM 187>.A<NA 2>
> > This error may be due to faulty Connection atoms.
> > !FATAL ERROR----------------------------------------
> > !FATAL: In file [chirality.c], line 142
> > !FATAL: Message: Atom named O1 from HEM did not match !
> > !
> > !ABORTING.
> >
> > On Sun, Jul 2, 2017 at 11:57 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > wrote:
> >
> >> Hi everyone
> >> I am trying to load pdb file that consist of heme---O2 through xleap i
> >> use these commands
> >> source leaprc.protein.ff14SB
> >> source leaprc.gaff
> >> loadamberparams argn.frcmod
> >> loadamberprep argn.in
> >> loadpdb oxyhem.pdb
> >>
> >> xleap close
> >> and these error show on terminal window after closing xleap
> >> +--- Sp0 probably means a new atom type is involved
> >> +--- which needs to be added via addAtomTypes
> >> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> >> +---Tried to superimpose torsions for: *-NC-FE-*
> >> +--- With Sp2 - Sp0
> >> +--- Sp0 probably means a new atom type is involved
> >> +--- which needs to be added via addAtomTypes
> >> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> >> +---Tried to superimpose torsions for: *-FE-ND-*
> >> +--- With Sp0 - Sp0
> >> +--- Sp0 probably means a new atom type is involved
> >> +--- which needs to be added via addAtomTypes
> >> !FATAL ERROR----------------------------------------
> >> !FATAL: In file [chirality.c], line 142
> >> !FATAL: Message: Atom named O1 from HEM did not match !
> >> !
> >> !ABORTING.
> >>
> >>
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>
>
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Received on Sun Jul 02 2017 - 21:30:03 PDT
