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 - 15:00:04 PDT
