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
>
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Received on Sun Jul 17 2016 - 11:30:02 PDT
