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.
>
> 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
>> >
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
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>>
>
>
>
> --
> 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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Received on Mon Jul 18 2016 - 03:30:02 PDT
