WARNING: There is a bond of 0.358135 angstroms between:
------- .R<IAS 231>.A<OD1 12> and .R<HIE 232>.A<N 1>
ERROR: The unperturbed charge of the unit: -1.032900 is not integral.
WARNING: The unperturbed charge of the unit: -1.032900 is not zero.
-- ignoring the error and warnings.
Building topology.
Building atom parameters.
For atom: .R<IAS 231>.A<H 2> Could not find vdW (or other) parameters
for type: h
For atom: .R<IAS 231>.A<OD1 12> Could not find vdW (or other)
parameters for type: o2
Parameter file was not saved.
Total unperturbed charge: -1.032900
Total perturbed charge: -1.032900
Writing pdb file: hpimt_leap.pdb
Converting N-terminal residue name to PDB format: NALA -> ALA
Converting C-terminal residue name to PDB format: CLYS -> LYS
Converting N-terminal residue name to PDB format: NVAL -> VAL
Converting C-terminal residue name to PDB format: CALA -> ALA
Quit
On Mon, Feb 22, 2016 at 2:48 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> If you copy your leap session with error messages, it could help to see
> what you did and the result.
>
> Bill
>
> On 2/22/16 1:15 AM, Jesmita Dhar wrote:
>> Dear Sir/Madam,
>> I want to simulate a complexed protein docked
>> with a peptide that contain an isoaspartic acid. I have used
>> antechember. But the parameter file I got, can not be used to generate
>> topology file for the complexed protein using leap. I would be helpful
>> if you can guide me to generate the parameter file for the isoaspartic
>> acid.
>> Waiting for your reply..
>>
>> Thanks
>>
>> Jesmita Dhar
>>
>> SRF,Bose Institute
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Feb 22 2016 - 02:30:03 PST
