I shall follow your instructions and tutorials sir Thank you so Much for
taking your time.
Kind Regards.
On Tue, Jul 11, 2017 at 5:57 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> I give up - you do not seem to understand anything I write.
>
> Bill
>
>
> On 7/11/17 2:52 PM, Rana Rehan Khalid wrote:
> > Dear Sir I actually read some previous threads about similar kind of
> > problem in which (some one suggested that we can ignore these thats why i
> > asked i saw the advice on the end of output) so when i tried to prepared
> > the parmtop and crd file then this output shows. and files created.
> > Checking Unit.
> > WARNING: There is a bond of 64.665185 angstroms between:
> > ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<NA 2>
> > WARNING: There is a bond of 63.582771 angstroms between:
> > ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<O1 74>
> > WARNING: There is a bond of 62.142422 angstroms between:
> > ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<NB 23>
> > WARNING: There is a bond of 60.983924 angstroms between:
> > ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<NC 39>
> > WARNING: There is a bond of 63.580412 angstroms between:
> > ------- .R<HEO 187>.A<FO 1> and .R<HEO 187>.A<ND 55>
> > WARNING: The unperturbed charge of the unit: -12.000000 is not zero.
> >
> > -- ignoring the warnings.
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Building proper torsion parameters.
> > Building improper torsion parameters.
> > old PREP-specified impropers:
> > <HEO 187>: NA C1A C4A FO
> > <HEO 187>: NB C1B C4B FO
> > <HEO 187>: NC C1C C4C FO
> > <HEO 187>: ND C1D C4D FO
> > <HEO 187>: C1A C2A NA CHA
> > <HEO 187>: C1B C2B NB CHB
> > <HEO 187>: C1C C2C NC CHC
> > <HEO 187>: C1D C2D ND CHD
> > <HEO 187>: C2A C3A C1A CAA
> > <HEO 187>: C2B C3B C1B CMB
> > <HEO 187>: C2C C3C C1C CMC
> > <HEO 187>: C2D C3D C1D CMD
> > <HEO 187>: C3A C4A C2A CMA
> > <HEO 187>: C3B C4B C2B CAB
> > <HEO 187>: C3C C4C C2C CAC
> > <HEO 187>: C3D C4D C2D CAD
> > <HEO 187>: C4A NA C3A CHB
> > <HEO 187>: C4B NB C3B CHC
> > <HEO 187>: C4C NC C3C CHD
> > <HEO 187>: C4D ND C3D CHA
> > total 627 improper torsions applied
> > 20 improper torsions in old prep form
> > Building H-Bond parameters.
> > Incorporating Non-Bonded adjustments.
> > Not Marking per-residue atom chain types.
> > Marking per-residue atom chain types.
> > (Residues lacking connect0/connect1 -
> > these don't have chain types marked:
> >
> > res total affected
> >
> > CSER 1
> > NMET 1
> > )
> > (no restraints)
> >
> > On Tue, Jul 11, 2017 at 5:36 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> The program is written to give you advice when there is a problem.
> >>
> >> The message you seem to not read is telling you to use addAtomTypes.
> >>
> >> Please try to read all the output carefully for understanding. It was
> >> written with you in mind.
> >>
> >> Bill
> >>
> >>
> >> On 7/11/17 2:30 PM, Rana Rehan Khalid wrote:
> >>> No advice in this thread. I check it maybe it is in my previous
> threads.
> >>> Thanks
> >>>
> >>> On Tue, Jul 11, 2017 at 5:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>
> >>>> The advice I quoted from your output:
> >>>>
> >>>> +--- Sp0 probably means a new atom type is involved
> >>>> +--- which needs to be added via addAtomTypes
> >>>>
> >>>> On 7/11/17 2:23 PM, Rana Rehan Khalid wrote:
> >>>>> Which one advice Sir
> >>>>>
> >>>>> On Tue, Jul 11, 2017 at 5:20 PM, Bill Ross <ross.cgl.ucsf.edu>
> wrote:
> >>>>>
> >>>>>> Did you follow that advice?
> >>>>>>
> >>>>>> Bill
> >>>>>>
> >>>>>>
> >>>>>> On 7/11/17 2:05 PM, Rana Rehan Khalid wrote:
> >>>>>>> +--- Sp0 probably means a new atom type is involved
> >>>>>>> +--- which needs to be added via addAtomTypes
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Received on Tue Jul 11 2017 - 15:30:02 PDT
