Hi Vishal,
2016-07-18 12:09 GMT+02:00 Vishal Nemaysh <vishal.bioinfotech.gmail.com>:
> Sir i have also attached the lig.mol2 and lig.frcmod file which i have
> used.
>
> On Mon, Jul 18, 2016 at 3:01 PM, Vishal Nemaysh <
> vishal.bioinfotech.gmail.com> wrote:
>
> > Respected Sir,
> >
> > plz help me regarding this problem i can't able to short out the same as
> i
> > have chacked as you suggested to me, but i can't find out the exect
> > solution. please kindly help me.
>
As Hai suggested, look into the amber mailing list. Such error have been
addressed already.
or
Can you please give more details of steps you have done. It seems you have
some missing parameters in your .frcmod file (lines with ATTN, need
revision).
Regards,
>
> > On Sun, Jul 17, 2016 at 11:45 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> Hi,
> >>
> >> this is a typical error. Can you try to follow those first
> >>
> >> http://archive.ambermd.org/201004/0574.html
> >>
> >> other topics
> >>
> >>
> https://www.google.com/search?q=WARNING%3A+There+is+a+bond+of+11.055252+angstroms+between%3A&rlz=1C1CHMO_enUS485US485&oq=WARNING%3A+There+is+a+bond+of+11.055252+angstroms+between%3A&aqs=chrome..69i57j69i58&sourceid=chrome&ie=UTF-8#q=WARNING:+There+is+a+bond+of+angstroms+between
> >> :
> >>
> >> Hai
> >>
> >> On Sun, Jul 17, 2016 at 1:52 PM, Vishal Nemaysh <
> >> vishal.bioinfotech.gmail.com> wrote:
> >>
> >> > Respected Sir,
> >> > I have faced the problem when i saved the
> .prmtop
> >> > and .inpcrd fileby appling the following command: but it will showed
> the
> >> > following error. how can i resolve it. the pdb complex file is
> attached
> >> > herewith plz check the same.
> >> >
> >> > *> saveamberparm b comp-lig_w_ions.prmtop comp-lig_w_ions.inpcrd*
> >> > Checking Unit.
> >> > WARNING: There is a bond of 11.055252 angstroms between:
> >> > ------- .R<NLEU 1>.A<CD1 12> and .R<UNK 364>.A<C14 12>
> >> > WARNING: There is a bond of 13.966544 angstroms between:
> >> > ------- .R<NLEU 1>.A<CG 10> and .R<UNK 364>.A<C16 11>
> >> > WARNING: There is a bond of 13.213808 angstroms between:
> >> > ------- .R<ARG 5>.A<C 23> and .R<UNK 364>.A<C23 1>
> >> > WARNING: There is a bond of 15.593765 angstroms between:
> >> > ------- .R<ARG 5>.A<CB 5> and .R<UNK 364>.A<C24 3>
> >> >
> >> > -- ignoring the warnings.
> >> >
> >> > Building topology.
> >> > Building atom parameters.
> >> > Building bond parameters.
> >> > Could not find bond parameter for: 3C - C*
> >> > Could not find bond parameter for: C - CZ
> >> > Could not find bond parameter for: C8 - CZ
> >> > Building angle parameters.
> >> > Could not find angle parameter: CT - 3C - C*
> >> > Could not find angle parameter: CT - 3C - C*
> >> > Could not find angle parameter: CT - CC - C*
> >> > Could not find angle parameter: HC - 3C - C*
> >> > Could not find angle parameter: 3C - CT - CC
> >> > Could not find angle parameter: 3C - C* - C*
> >> > Could not find angle parameter: 3C - C* - CC
> >> > Could not find angle parameter: 2C - 3C - C*
> >> > Could not find angle parameter: O - C - CZ
> >> > Could not find angle parameter: C - CZ - NT
> >> > Could not find angle parameter: C8 - C8 - CZ
> >> > Could not find angle parameter: HC - C8 - CZ
> >> > Could not find angle parameter: HC - C8 - CZ
> >> > Could not find angle parameter: C8 - CZ - NT
> >> > Could not find angle parameter: CX - C8 - CZ
> >> > Could not find angle parameter: CX - C - CZ
> >> > Could not find angle parameter: N - C - CZ
> >> > Building proper torsion parameters.
> >> > ** No torsion terms for HC-CT-3C-C*
> >> > ** No torsion terms for HC-CT-3C-C*
> >> > ** No torsion terms for HC-CT-3C-C*
> >> > ** No torsion terms for CT-3C-CT-CC
> >> > ** No torsion terms for CT-3C-C*-C*
> >> > ** No torsion terms for CT-3C-C*-CC
> >> > ** No torsion terms for HC-CT-3C-C*
> >> > ** No torsion terms for HC-CT-3C-C*
> >> > ** No torsion terms for HC-CT-3C-C*
> >> > ** No torsion terms for CT-3C-C*-C*
> >> > ** No torsion terms for CT-3C-C*-CC
> >> > ** No torsion terms for CT-CC-C*-C
> >> > ** No torsion terms for CT-CC-C*-C*
> >> > ** No torsion terms for HC-3C-CT-CC
> >> > ** No torsion terms for HC-3C-C*-C*
> >> > ** No torsion terms for HC-3C-C*-CC
> >> > ** No torsion terms for 3C-C*-C*-C
> >> > ** No torsion terms for 3C-C*-C*-CC
> >> > ** No torsion terms for 3C-C*-CC-NA
> >> > ** No torsion terms for 3C-C*-CC-CZ
> >> > ** No torsion terms for HC-2C-3C-C*
> >> > ** No torsion terms for HC-2C-3C-C*
> >> > ** No torsion terms for 2C-3C-CT-CC
> >> > ** No torsion terms for 2C-3C-C*-C*
> >> > ** No torsion terms for 2C-3C-C*-CC
> >> > ** No torsion terms for CX-2C-3C-C*
> >> > ** No torsion terms for O-C-CZ-NT
> >> > ** No torsion terms for C-CZ-NT-CZ
> >> > ** No torsion terms for C-CZ-NT-CZ
> >> > ** No torsion terms for C8-C8-CZ-NT
> >> > ** No torsion terms for HC-C8-CZ-NT
> >> > ** No torsion terms for HC-C8-CZ-NT
> >> > ** No torsion terms for C8-CZ-NT-CZ
> >> > ** No torsion terms for C8-CZ-NT-CZ
> >> > ** No torsion terms for CX-C8-CZ-NT
> >> > ** No torsion terms for CX-C-CZ-NT
> >> > ** No torsion terms for N-C-CZ-NT
> >> > ** No torsion terms for C*-3C-CT-CC
> >> > Building improper torsion parameters.
> >> > old PREP-specified impropers:
> >> > <UNK 364>: C18 C20 N19 H39
> >> > <UNK 364>: C15 N19 C18 O28
> >> > <UNK 364>: C16 C18 C15 C14
> >> > total 1146 improper torsions applied
> >> > 3 improper torsions in old prep form
> >> > Building H-Bond parameters.
> >> > Incorporating Non-Bonded adjustments.
> >> > Parameter file was not saved.
> >> > >
> >> >
> >> > thankyou in advance....
> >> >
> >> > --
> >> > Vishal Nemaysh
> >> > Research Scholar,
> >> > Neuropharmaceutical Chemistry Group,
> >> > Dr. B. R. Ambedkar Center for Biomedical Research,
> >> > University of Delhi, Delhi-110007
> >> > Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> >> > Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Vishal Nemaysh
> > Research Scholar,
> > Neuropharmaceutical Chemistry Group,
> > Dr. B. R. Ambedkar Center for Biomedical Research,
> > University of Delhi, Delhi-110007
> > Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
> >
>
>
>
> --
> Vishal Nemaysh
> Research Scholar,
> Neuropharmaceutical Chemistry Group,
> Dr. B. R. Ambedkar Center for Biomedical Research,
> University of Delhi, Delhi-110007
> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
*Bilal Nizami*
School of Health Sciences
University of KwaZulu-Natal
Durban
4000
South Africa
Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
Email: 214573074.stu.ukzn.ac.za
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Received on Mon Jul 18 2016 - 05:00:02 PDT
