[AMBER] Regarding Parameter file not saved

From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
Date: Sun, 17 Jul 2016 23:22:32 +0530

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 - 11:00:02 PDT
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