Add ions in leap if you want neutrality ('help addions').
Bill
On 8/28/17 9:06 AM, Bill Ross wrote:
> Have you looked at the long bond in your pdb file?
>
> Try 'desc NMET' in leap to see correct atom names, and edit the 'H' atom
> name in the pdb resideu 82 NMET to have the right name.
>
> Bill
>
>
> On 8/28/17 9:03 AM, Ashok Kumar wrote:
>> Dear All,
>>
>> I want to create topology file for protei-ligand complex, but it
>> display the below error
>>
>> WARNING: There is a bond of 3.672093 angstroms between:
>> ------- .R<NMET 82>.A<C 18> and .R<NMET 82>.A<CA 5>
>> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
>> FATAL: Atom .R<NMET 82>.A<H 20> does not have a type.
>> Failed to generate parameters
>> Parameter file was not saved.
>>
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Received on Mon Aug 28 2017 - 09:30:04 PDT
